System, method, and device for the expression or repression of proteins

ABSTRACT

This invention relates to systems, methods, and devices for inducing and/or repressing the expression of proteins. More particularly, the invention relates to systems, methods, and devices for inducing and/or repressing the expression of proteins in plastids. An exemplary embodiment involves the regulation of the expression of proteins involved in hydrogen production to stimulate the production of hydrogen gas using the methods, systems, and devices described herein.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a U.S. national application under 37 C.F.R. §371(b)of International Application Serial No. PCT/US2007/017774 filed Aug. 11,2007, which claims priority under 35 U.S.C §119(e) to U.S. ProvisionalApplication Ser. No. 60/837,001, filed on Aug. 11, 2006, incorporatedherein by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-Web and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Aug. 12, 2011, isnamed 12377238SequenceListingCRF.txt and is 16,191 bytes in size.

FIELD OF THE INVENTION

This invention relates to systems, methods, and devices for inducingand/or repressing the expression of proteins. More particularly, theinvention relates to systems, methods, and devices for inducing and/orrepressing the expression of proteins in plastids.

BACKGROUND AND SUMMARY OF THE INVENTION

Proteins (e.g., peptides, oligopeptides, and polypeptides) areresponsible for most of the activities of a cell, such as catalysis,communication, defense, movement, and transport. The underlying basis ofa protein's biological activity is its amino acid sequence and/or itsconformation. Accordingly, the biologically active portion of a proteinshould remain essentially intact and in its biologically functionalconformation. The advancements in genetic engineering techniques forprotein expression have led to the development of methods for thecontrolled expression of both native and foreign proteins in varioussystems in a form that maintains the biological activity of theproteins. Such genetically engineered, controlled expression systems canresult in higher protein yield due to the expression of properly-folded,stable proteins where inactivation and degradation of the proteins isreduced as a result of the ability to control protein expression.

Although a number of different types of expression systems have beendeveloped, in various organelles of host cells such as microorganisms,eukaryotic cells, including fungi, yeast, and mammalian cells, insectcells, etc., an expression system for the controlled expression ofproteins utilizing stability factors of nuclear origin to regulate theexpression of proteins in plastids has not previously been developed.Plastids are organelles responsible for photosynthesis and are commonlyclassified as chloroplasts, leucoplasts, amyloplasts, or chromoplasts.Plastids can differentiate or redifferentiate between these forms.

In one embodiment, a method for preparing an expression system forinducing the production of a protein in the plastid of a cell isprovided. The method comprises the steps of introducing a first nucleicacid into the nucleus of a cell wherein the first nucleic acid encodesan inducible promoter, operatively linking the first nucleic acid to asecond nucleic acid to form a recombinant nucleic acid wherein thesecond nucleic acid encodes a stability factor, wherein the introductionof an inducer or the removal of a repressor induces the expression ofthe stability factor, wherein the expressed stability factor associatesin the plastid with an untranslated region of an mRNA stabilized by thestability factor and transcribed from a third nucleic acid, wherein thethird nucleic acid is either native to the plastid or is foreign to theplastid and wherein the third nucleic acid encodes the protein, andwherein expression of the mRNA results in the production of the protein.

In another illustrative embodiment, a method for preparing an expressionsystem for repressing the expression of a plastid protein in the plastidof a cell is provided. The method comprises the steps of introducing afirst nucleic acid into the nucleus of a cell wherein the first nucleicacid encodes a repressible promoter, operatively linking the firstnucleic acid to a second nucleic acid to form a recombinant nucleic acidwherein the second nucleic acid encodes a stability factor, wherein theintroduction of a repressor or the removal of an inducer represses theexpression of the stability factor, and wherein the repression of theexpression of the stability factor results in the repression ofexpression of an mRNA stabilized by the stability factor and transcribedfrom a third nucleic acid, wherein the third nucleic acid is eithernative to the plastid or is foreign to the plastid and wherein the thirdnucleic acid encodes the protein, and wherein the expression of theprotein is repressed.

In still another illustrative aspect, a method for expressing a plastidprotein in the plastid of a cell is provided. The method comprises thesteps of contacting the cell with an inducer or treating the cell underconditions that result in the removal of a repressor, wherein theinducer or the repressor associates with a first nucleic acid in thenucleus, wherein the first nucleic acid encodes an inducible promoter,wherein the first nucleic acid is operatively linked to a second nucleicacid to form a recombinant nucleic acid and wherein the second nucleicacid encodes a stability factor, expressing the stability factor,introducing the stability factor into the plastid wherein the stabilityfactor associates in the plastid with an untranslated region of an mRNAto stabilize the mRNA wherein the mRNA is transcribed from a thirdnucleic acid which is either native to the plastid or is foreign to theplastid and wherein the third nucleic acid encodes the protein,expressing the mRNA, and producing the protein in the plastid.

In another embodiment, a method for repressing the expression of aplastid protein in the plastid of a cell is provided. The methodcomprises the steps of contacting the cell with a repressor or treatingthe cell under conditions that result in the removal of an inducer,wherein the repressor or the inducer associates with a first nucleicacid in the nucleus of the cell, wherein the first nucleic acid encodesa repressible promoter, wherein the first nucleic acid is operativelylinked to a second nucleic acid to form a recombinant nucleic acid, andwherein the second nucleic acid encodes a stability factor, repressingthe expression of the stability factor wherein the stability factorassociates in the plastid with an untranslated region of an mRNA tostabilize the mRNA wherein the mRNA is transcribed from a third nucleicacid which is either native to the plastid or is foreign to the plastidand wherein the third nucleic acid encodes the protein, repressing theexpression of an mRNA, and repressing the expression of the protein.

In still another embodiment, a system for expressing a plastid proteinin the plastid of a recombinant host cell is provided. The systemcomprises an exogenously added inducer that induces the expression of anuclear protein, the recombinant host cell wherein the nucleus of therecombinant host cell comprises a recombinant nucleic acid, wherein therecombinant nucleic acid comprises a first nucleic acid operativelylinked to a second nucleic acid to form the recombinant nucleic acid,wherein the first nucleic acid encodes an inducible promoter and whereinthe second nucleic acid encodes a stability factor, and the plastidcomprising a third nucleic acid that is either native to the plastid orforeign to the plastid wherein the third nucleic acid encodes theexpressed plastid protein wherein the expression of the mRNA encodingthe plastid protein is controlled by the stability factor.

In another illustrative embodiment, a system for repressing theexpression of a plastid protein in the plastid of a recombinant hostcell is provided. The system comprises an exogenously added repressorthat represses the expression of a nuclear protein, the recombinant hostcell wherein the nucleus of the recombinant host cell comprises arecombinant nucleic acid, wherein the recombinant nucleic acid comprisesa first nucleic acid operatively linked to a second nucleic acid to formthe recombinant nucleic acid, wherein the first nucleic acid encodes arepressible promoter and wherein the second nucleic acid encodes astability factor, and the plastid comprising a third nucleic acid thatis either native to the plastid or foreign to the plastid wherein thethird nucleic acid encodes the expressed plastid protein and wherein theexpression of the mRNA encoding the protein is controlled by thestability factor.

In another embodiment, a method for stimulating the production ofhydrogen gas by expressing a plastid protein in the plastid of a cell isprovided. The method comprises the steps of contacting the cell with aninducer or treating the cell under conditions that result in the removalof a repressor, wherein the inducer or the repressor associates with afirst nucleic acid in the nucleus, wherein the first nucleic acidencodes an inducible promoter, wherein the first nucleic acid isoperatively linked to a second nucleic acid to form a recombinantnucleic acid and wherein the second nucleic acid encodes a stabilityfactor, expressing the stability factor, introducing the stabilityfactor into the plastid wherein the stability factor associates in theplastid with an untranslated region of an mRNA to stabilize the mRNAwherein the mRNA is transcribed from a third nucleic acid which iseither native to the plastid or is foreign to the plastid wherein thethird nucleic acid encodes the protein, expressing the mRNA, producingthe protein in the plastid, and producing hydrogen gas.

In yet another embodiment, a method for inhibiting the production ofhydrogen gas by repressing the expression of a plastid protein in theplastid of a cell is provided. The method comprises the steps ofcontacting the cell with a repressor or treating the cell underconditions that result in the removal of an inducer, wherein therepressor or the inducer associates with a first nucleic acid in thenucleus of the cell, wherein the first nucleic acid encodes arepressible promoter, wherein the first nucleic acid is operativelylinked to a second nucleic acid to form a recombinant nucleic acid,wherein the second nucleic acid encodes a stability factor, repressingthe expression of the stability factor wherein the stability factorassociates in the plastid with an untranslated region of an mRNA tostabilize the mRNA wherein the mRNA is transcribed from a third nucleicacid which is either native to the plastid or is foreign to the plastidand wherein the third nucleic acid encodes the protein, repressing theexpression of the mRNA, repressing the expression of the protein, andinhibiting the production of hydrogen gas.

In still another embodiment, a method for stimulating the production ofhydrogen gas by inducing and repressing the expression of a plastidprotein in the plastid of a cell is provided. The method comprises thesteps of sequentially i) contacting the cell with an inducer or treatingthe cell under conditions that result in the removal of a repressor andii) contacting the cell with the repressor or treating the cell underconditions that result in the removal of the inducer, wherein theinducer or the repressor associates with a first nucleic acid in thenucleus, wherein the first nucleic acid encodes an inducible promoter,wherein the first nucleic acid is operatively linked to a second nucleicacid to form a recombinant nucleic acid and wherein the second nucleicacid encodes a stability factor, sequentially expressing and repressingthe expression of the stability factor, wherein the stability factorassociates in the plastid with an untranslated region of an mRNA tostabilize the mRNA wherein the mRNA is transcribed from a third nucleicacid which is either native to the plastid or is foreign to the plastidwherein the third nucleic acid encodes the protein, sequentiallyexpressing and repressing the expression of the mRNA, producing theprotein in the plastid, and producing hydrogen gas.

In any of the above-described embodiments, the first nucleic acid can beoperatively linked to the second nucleic acid to form the recombinantnucleic acid prior to introducing the recombinant nucleic acid into thenucleus, the cell can have an inoperative copy or can be missing a copyor a homolog of the second or the third nucleic acid, the cell can be aplant cell or an algal cell, the plastid can be selected from the groupconsisting of a chloroplast, a leucoplast, a amyloplast, an etioplast,an elaioplast, and a chromoplast, the inducible promoter can have atleast 90% sequence similarity to the Cyc6 promoter, and the thirdnucleic acid can encode a gene that has at least 90% sequence similarityto the psbD gene.

In any of the above-described embodiments, the inducer or repressor canbe a chemical or an environmental condition where the chemical can becopper and where the environmental condition can be reduction in theconcentration of oxygen to a predetermined level, the inducer can beapplied and removed for a plurality of cycles wherein a cycle comprisesapplying and removing the inducer, the protein can be a protein involvedin photosynthesis or in the production of hydrogen gas, the protein canbe selected from the group consisting of a pharmaceutical agent, anindustrial enzyme, an enzyme involved in chloroplast maturation ordegradation, and a nutraceutical where the pharmaceutical agent isselected from the group consisting of an antibody, a vaccine antigen,and an antimicrobial agent, or other defense products for the host celland the stability factor can be selected from the group consisting ofNac2 and Mbb1. In another illustrative embodiment, the second nucleicacid can code for a translational activating factor, such as, forexample, Tbc2 or Tca1.

In another embodiment of the invention, a system and method forregulating the expression or repression of native or foreign genes inplastids is provided. In one embodiment, the invention relates to anexpression system employing a nuclear-encoded chloroplast transcriptionfactor, Nac2, the expression of which is regulated by an induciblepromoter of the Cyc6 gene. In another embodiment, induction of Nac2expression by an inducer (i.e., an agent or alteration of anenvironmental condition), such as low levels of oxygen, causes theexpression of the psbD gene in the chloroplast. In yet anotherembodiment, an agent or environmental condition, such as removal ofcopper, that causes induction of the Cyc6 promoter, also causesexpression of the psbD gene. In another illustrative embodiment,repression of the Nac2 gene by a repressor (i.e., an agent or alterationof an environmental condition), such as high levels of oxygen, resultsin no or reduced expression of the psbD gene. In a related embodiment,an agent or alteration in an environmental condition that represses theinducible Cyc6 promoter also causes reduced expression of the psbD gene.

In other illustrative embodiments, the invention relates to theinducible expression of or the repression of a foreign gene in thechloroplast whereby replacement of the psbD gene in the chloroplast witha foreign gene facilitates inducible expression of or the repression ofthe foreign gene in the chloroplast by regulation of Nac2 expression.

In another embodiment, the invention relates to a method of producinghydrogen gas in the chloroplast through regulation of the psbD gene byNac2 expression or repression of expression of Nac2. In thisillustrative aspect of the invention, environmental conditions thatfacilitate the induction and repression of the Nac2 gene (e.g., reducingthe level of oxygen to induce expression and elevating the level ofoxygen to repress expression), resulting in the oscillating inductionand repression of psbD gene expression, result in a reduction in therate of photosynthesis and a resulting reduction in the concentration ofoxygen. In this embodiment, the reduction in the concentration of oxygenfacilitates the production of hydrogen. Thus, in one embodiment, theinvention relates to a method of producing hydrogen gas by regulatingthe oscillating induction and repression of Nac2 and psbD geneexpression.

In yet another embodiment, the invention relates to a method forenhancing the hydrogen-generating system through the recombinantexpression of other genes in the chloroplast, for example, hydrogenasesand repression of other recombinant or native proteins, such asphosphoribulose kinase.

In still another embodiment an apparatus for the production of hydrogenis provided. The apparatus comprises a first vessel configured to hold acell culture in a substantially oxygen-depleted environment, a firstpump in fluid communication with the first vessel and configured to pumpa medium into the first vessel at a predetermined rate, and a measuringdevice coupled to the first vessel and configured to measure an amountof hydrogen produced by the cell culture.

In this embodiment, the first pump can be configured to pump the amountof medium into the first vessel at a rate substantially equal to therate of growth of the cell culture, the first pump can comprise aperistaltic pump, the cell culture can comprise a cy6Nac2.49 culture,the measuring device can comprise a mass spectrometer, the apparatus canfurther comprise an agitation device coupled to the first vessel andoperable to agitate the cell culture, the agitation device can comprisea magnetic stir bar, the apparatus can further comprise a second vesselconfigured to hold an amount of the medium, wherein the first pump isfluidly coupled to the second vessel and configured to pump the mediumfrom the second vessel at the predetermined rate, the apparatus canfurther comprise a third vessel in fluid communication with the firstvessel and configured to hold an overflow of the medium from the firstvessel, and the apparatus can further comprise a filter and a secondpump in fluid communication with the third vessel and the second vessel,the second pump being configured to pump an amount of the medium fromthe third vessel, through the filter, and into the second vessel.

BRIEF DESCRIPTION OF THE DRAWINGS

The present invention may be more readily understood by reference to thefollowing figures wherein:

FIG. 1 shows a diagram of hydrogen and electron flow in the chloroplastof C. reinhardtii under aerobic and anaerobic conditions (from Kruse etal., 2005).

FIG. 2 shows a schematic outline of a plastid gene regulation system inwhich the nuclear inducible promoter is induced in the presence of aninducer. The left-hatched box represents the nuclear inducible promoterand the right-hatched box represents the gene for the stability factor.The filled box represents the stability factor association element, inthis embodiment located in the 5′ untranslated region of the plastidmRNA. The open box represents an mRNA produced from a plastid nativegene. The cross-hatched box represents an mRNA produced from a foreigngene in the plastid.

FIG. 3 shows a schematic outline of a plastid gene regulation system inwhich the nuclear inducible promoter is repressed in the absence of aninducer. The left-hatched box represents the nuclear inducible promoterand the right-hatched box represents the gene for the stability factor.The filled box represents the stability factor association element, inthis embodiment located in the 5′ untranslated region of the plastidmRNA. The open box represents an mRNA produced from a plastid nativegene. The cross-hatched box represents an mRNA produced from a foreigngene in the plastid.

FIG. 4 shows a schematic outline of a plastid gene regulation system inwhich the nuclear repressible promoter is repressed in the presence of arepressor. The left-hatched box represents the nuclear repressiblepromoter and the right-hatched box represents the gene for the stabilityfactor. The filled box represents the stability factor associationelement, in this embodiment located in the 5′ untranslated region of theplastid mRNA. The open box represents an mRNA produced from a plastidnative gene. The cross-hatched box represents an mRNA produced from aforeign gene in the plastid.

FIG. 5 shows a schematic outline of a plastid gene regulation system inwhich the nuclear repressible promoter is induced in the absence arepressor. The left-hatched box represents the nuclear repressiblepromoter and the right-hatched box represents the gene for the stabilityfactor. The filled box represents the stability factor associationelement, in this embodiment located in the 5′ untranslated region of theplastid mRNA. The open box represents an mRNA produced from a plastidnative gene. The cross-hatched box represents an mRNA produced from aforeign gene in the plastid.

FIG. 6 shows a schematic of the Chlamydomonas chloroplast genome withthe psbD gene location shown. The arrow indicates the site of insertionof pSK108.

FIG. 7 shows a flow diagram for an apparatus for producing hydrogen.

FIG. 8 shows an apparatus for producing hydrogen.

FIG. 9 shows a schematic of the nuclear expression vector pSL17 used totransform nuclear Nac2 mutants and to introduce the Cyc6 promoter andthe Nac2 gene. The map shows the arrangement of promoters, enhancerelement from HSP70A promoter, and restriction sites for inserting theCyc6 promoter and Nac2 gene. FIG. 9 discloses the “BstXI” sequence asSEQ ID NO: 9.

FIG. 10 shows a schematic of cy6Nac2(paroR).

FIGS. 11 a-c show the genomic sequence of the Nac2 midi gene. (SEQ IDNO:10). The initiation codon is the first underlined ATG. The putativetransit peptide is also underlined.

FIG. 12 shows the Cyc6 genomic sequence (SEQ ID NO: 11). The genomicsequences used to generate the fusion construct with the Nac2 midi geneare underlined. Also indicated (double-underlining) is the threebase-pair difference in the cyc6Nac2 construct that created an NdeIrestriction site.

FIG. 13 shows the growth properties of the cy6Nac2.49 transgenic strain.

FIG. 14 shows Western blot analysis of the cy6Nac2.49 transgenic strain.

FIG. 15 shows the hydrogen production of the cy6Nac2.49 transgenicstrain.

FIG. 16 shows a map of the pSK108 vector. The pSK108 vector has flankingchloroplast DNA to direct it to the region surrounding the psbD gene.

FIG. 17 shows a map of pcg12.

FIG. 18 shows a map of the chloroplast expression plasmid pcg12 IBDVFlag.

FIG. 19 shows a map of the chloroplast expression plasmid pcg12 VP28Flag.

FIG. 20 shows the chloroplast DNA sequence of psbD. (SEQ ID NO: 12). Theunderlined sequences were used to drive the expression of genes in thechloroplast using the cyc6Nac2 system.

FIG. 21 shows isolation of IND_aadA_X transgenic strains and growth onvarious media.

FIG. 22 shows Northern blot analysis of total RNA extracted fromwild-type and isolation of IND_aadA_(—)117.

FIG. 23 shows analysis of total and soluble (α-Nac 2) extracted fromwild type and IND_aadA_(—)117.

FIG. 24 shows screening for transgenic strains that induced theexpression of three foreign proteins (DILP, IBVD, and VP28).

FIG. 25 shows inducible production of a foreign protein (DILP) using theNac2 inducible chloroplast gene expression system.

FIG. 26 shows accumulation of psbD RNA, D2 and Nac2 proteins incy6Nac2.49.

FIG. 27 shows restoration of constitutive PSII accumulation incy6Nac2.49 by replacement of the psbD 5′ UTR with the petA 5′ UTR.

FIG. 28 shows inducible expression of the chloroplast psbD gene.

FIG. 29 shows a time course of copper-mediated repression of PSIIsynthesis in cy6Nac2.49.

FIG. 30 shows a time course of accumulation of PSII in cy6Nac2.49.

FIG. 31 shows expression of the psbD-aadA gene is induced by copperdepletion and repressed by copper in the IND_aadA_(—)117 transformants.

FIG. 32 shows hydrogen production in the cy6Nac2-49 strain.

DETAILED DESCRIPTION OF THE ILLUSTRATIVE EMBODIMENTS

As used herein, the phrase “foreign gene” or “foreign nucleic acid”(i.e., a transgene) means any nucleic acid inserted into a nucleic acidof a cell using recombinant DNA technology where the foreign gene orforeign nucleic acid is not normally present in that location in thecell. A foreign gene or foreign nucleic acid can include coding andnoncoding nucleic acid sequences. A foreign gene or foreign nucleic acidcan comprise a native nucleic acid that has been modified usingrecombinant DNA technology and has been reintroduced into the cell, orcan comprise a native nucleic acid moved from one location to anotherwithin the cell.

As used herein, the phrase “native nucleic acid” or “native gene” meansa nucleic acid that has its natural sequence (including naturallyoccurring mutations) and location in a cell.

As used herein, the term “inducible” means a promoter capable of beingregulated so that mRNA transcripts are produced. Methods for determiningthe level of mRNA transcripts include Northern blotting and real-timePCR.

As used herein, the term “expression” can mean transcription of DNA intoRNA or translation of RNA into protein.

As used herein the phrase “stability factor” means a nuclear proteinthat can exhibit activities, including, but not limited to,transcriptional, post-transcriptional, translational,post-translational, protein targeting, and protein recruitmentactivities, to enhance the expression or activity of a chloroplastprotein.

The invention relates to systems, methods, and devices for theregulation of expression of a gene in the plastid of a cell (e.g., analgal or plant cell) for the purpose of producing useful products. Theinduction or repression of gene expression in the plastid isaccomplished by transforming the nuclear genome of the cell with aninducible or repressible promoter operatively linked to a gene whichcodes for a chloroplast-targeted protein. The chloroplast-targetedprotein associates, directly or indirectly (e.g., through accessoryproteins), with an untranslated region of a plastid-expressed mRNA. Thechloroplast-targeted protein is required for stability and/ortranslation of the plastid-expressed mRNA and hence expression of theplastid gene.

In one embodiment, the nuclear promoter is an inducible promoter and theaddition or removal of a chemical (e.g., copper, a carbohydrate, or aprotein) compound or an alteration in an environmental condition (e.g.,low oxygen concentration, or an alteration in light, temperature, ornutritional status) activates the promoter resulting in expression ofthe chloroplast mRNA, and subsequently, the expression of the proteincoded by the mRNA. In another embodiment, the nuclear promoter is arepressible promoter and the addition or removal of a chemical compound(e.g., copper, a carbohydrate, or a protein) or an alteration in anenvironmental condition (e.g., high oxygen concentration, or analteration in light, temperature, or nutritional status) represses thepromoter resulting in lack of expression of stability factor andinhibition of expression of the chloroplast mRNA, and subsequently, theexpression of the protein coded by the mRNA.

In one embodiment, the invention relates to a method for expressing aprotein in the plastid of a cell. The method comprises the steps ofcontacting the cell with an inducer or treating the cell underconditions that result in the removal of a repressor, wherein theinducer or the repressor associates with a first nucleic acid in thenucleus, wherein the first nucleic acid encodes an inducible promoter,wherein the first nucleic acid is operatively linked to a second nucleicacid to form a recombinant nucleic acid and wherein the second nucleicacid encodes a stability factor, expressing the stability factor,introducing the stability factor into the plastid wherein the stabilityfactor associates in the plastid with an untranslated region of an mRNAto stabilize the mRNA wherein the mRNA is transcribed from a thirdnucleic acid which is either native to the plastid or is foreign to theplastid and wherein the third nucleic acid encodes the protein,expressing the mRNA, and producing the protein in the plastid.

In another embodiment, a method for repressing the expression of aplastid protein in the plastid of a cell is provided. The methodcomprises the steps of contacting the cell with a repressor or treatingthe cell under conditions that result in the removal of an inducer,wherein the repressor or the inducer associates with a first nucleicacid in the nucleus of the cell, wherein the first nucleic acid encodesa repressible promoter, wherein the first nucleic acid is operativelylinked to a second nucleic acid to form a recombinant nucleic acid, andwherein the second nucleic acid encodes a stability factor, repressingthe expression of the stability factor wherein the stability factorassociates in the plastid with an untranslated region of an mRNA tostabilize the mRNA wherein the mRNA is transcribed from a third nucleicacid which is either native to the plastid or is foreign to the plastidand wherein the third nucleic acid encodes the protein, repressing theexpression of an mRNA, and repressing the expression of the protein.

In the above-described embodiments, the protein is expressed in theplastid of a cell. Illustratively, the cells can be cells of plants oralgal cells or any cell type that contains a plastid. Plastids areorganelles that contain a plastid genome, often in multiple copies.Plastids are found in, for example, plants and algae and includechloroplasts, leucoplasts, amyloplasts, etioplasts, elaioplasts, andchromoplasts.

In the method and system embodiments described herein, the third nucleicacid encodes the protein of interest. In one illustrative embodiment,the third nucleic acid, coding for the expressed protein, can be eithernative to the plastid or foreign to the plastid (i.e., a transgene). Inthis embodiment, the expressed protein (e.g., a peptide, anoligopeptide, or a polypeptide) can be expressed under the control of aninducible or repressible promoter and includes proteins involved inphotosynthesis, such as components of Photosystem I or II (e.g., psbAand psbD and the D1 and D2 subunits of Photosystem II), proteinsinvolved in CO₂ fixation (e.g., phosphoribulose kinase), hydrogenases(e.g., HydA1 and HydA2), and proteins that regulate the activity of anyof these proteins (e.g., the assembly of any these proteins (e.g., HydEFand HydG)), or any other proteins that are native to the plastid.Exemplary native proteins that can be expressed under the control of aninducible or repressible promoter include any of the proteins involvedin the regulation of the photosynthetic processes or carbon assimilationprocesses depicted or implied in FIG. 1 or any other protein native tothe plastid. In an alternate embodiment, an amino acid, such as anaromatic amino acid, or an amino acid precursor can be produced byregulating the expression of proteins native to the plastid that areinvolved in the synthetic pathways for amino acids, such as aromaticamino acids.

In another illustrative embodiment, a protein involved in the productionof hydrogen gas can be expressed under the control of an inducible orrepressible promoter, or both, using the methods, systems, and devicesdescribed herein. In this embodiment, proteins involved in theproduction of hydrogen gas can be any proteins described in this or thepreceding paragraph, or can be any of the proteins which are involved inthe regulation of the photosynthetic processes or carbon assimilationprocesses depicted or implied in FIG. 1. In this embodiment, the induceror repressor can be applied and removed for a plurality of cycles,wherein a cycle comprises applying and removing the inducer orrepressor.

In another embodiment, the third nucleic acid, coding for the expressedprotein, can be foreign to the plastid (i.e., a foreign nucleic acid ora foreign gene). In this embodiment, the protein can be a pharmaceuticalagent, an industrial enzyme, an enzyme involved in chloroplastmaturation or degradation, or a nutraceutical. In this embodiment, theexpressed protein can be, for example, an antibody, a vaccine antigen(e.g., for use in a vaccine), an antimicrobial agent, or other defenseproducts for the host cell, a growth hormone, a cytokine, such as aninterleukin or an interferon, insulin, colony-stimulating factors,coagulation factors, erythropoietins, growth factors, such as epidermalgrowth factor, somatotropin, fibroblast growth factor, platelet-derivedgrowth factor, and the like, amylases, proteases, lipases, pectinases,cellulases, hemicellulases, pentosanases, xylanases, and phytases,insecticidal proteins, phenyl ammonia lyase, or any other pharmaceuticalagent, industrial enzyme, or nutraceutical that is proteinaceous.

In yet another illustrative embodiment, additional nucleic acids (e.g.,a fourth nucleic acid, etc.) coding for an expressed protein, can beexpressed in the chloroplast and can be native or foreign to the plastid(i.e., a foreign nucleic acid or a foreign gene). In these embodiments,the expression of the additional nucleic acids can be controlled bytheir own stability factors coded by additional nucleic acids in thenucleus (i.e., similar to the second nucleic acid) or the expression ofthese additional nucleic acids can be controlled by the stability factorencoded by the second nucleic acid. In one illustrative embodiment, onestability factor associates with the stability factor associationelement in plastid mRNA and stimulates expression of the third nucleicacid and additional nucleic acids (e.g., the fourth nucleic acid, etc.)operatively linked to the third nucleic acid. In these embodiments, theprotein expressed can be a pharmaceutical agent, an industrial enzyme,an enzyme involved in chloroplast maturation or degradation, or anutraceutical. In this embodiment, the expressed protein can be, forexample, an antibody, a vaccine antigen (e.g., for use in a vaccine), anantimicrobial agent, or other defense products for the host cell, agrowth hormone, a cytokine, such as an interleukin or an interferon,insulin, colony-stimulating factors, coagulation factors,erythropoietins, growth factors, such as epidermal growth factor,somatotropin, fibroblast growth factor, platelet-derived growth factor,and the like, amylases, proteases, lipases, pectinases, cellulases,hemicellulases, pentosanases, xylanases, and phytases, insecticidalproteins, phenyl ammonia lyase, or any other pharmaceutical agent,industrial enzyme, or nutraceutical that is proteinaceous.

In the embodiment where the expressed protein is a vaccine antigen foruse as a vaccine, the expressed protein, or a portion thereof, can belocated on or in an organelle of the cells, such as algal or plantcells. The algae, for example, can then be lysed and the vaccine antigencan be used for inducing an immune response in a host animal to apathogen if the vaccine antigen is at least partially derived from apathogenic organism.

In one embodiment, the algae with the vaccine antigen are administeredas a food substance. Exemplary animals to which the vaccines can beadministered include, but are not limited to, mammals, birds, andaquaculture species. In particular, the vaccine can be administered toaquatic vertebrates such as all vertebrate fish, which may be bony orcartilaginous fish, including, but not limited to, salmonids (includingtrout, salmon, and Artic char), carp, catfish, yellowtail, seabream, andseabass. Such a vaccine can also be administered to shellfish including,but are not limited to, clams, lobster, shrimp, crab, and oysters.Exemplary methods of delivery include oral administration, as a driedpowder, as a component of the normal diet, and by immersion of theanimal in a suspension containing the vaccine.

In the case of aquatic vertebrates, examples of pathogenic organismswhose antigenic determinants may be expressed as vaccine antigens on thesurface of cells using the methods and systems described herein include,but are not limited to Rennibacterium salmoninarum (causative agent ofbacterial kidney disease in salmon, trout, char and whitefish; i.e.,salmonids), Aeromonas salmonicida, Aeromonas hydrophila, species ofVibrio (including V. anguillarum and V. ordalii), species of Pasteurella(including P. piscicida), species of Yersinia, species of Streptococcus,Edwardsiella tarda and Edwardsiella ictaluria, the viruses causing viralhemorrhagic septicemia, infectious pancreatic necrosis, viremia of carp,infectious hematopoietic necrosis virus, channel catfish virus, grasscarp hemorrhagic virus, nodaviridae such as nervous necrosis virus orstriped jack nervous necrosis virus, infectious salmon anaemia virus,and the parasites Ceratomyxa shasta, Ichthyophthirius multifillius,Cryptobia salmositica, Lepeophtheirus salmonis, Tetrahymena species,Trichodina species and Epistylus species.

In the embodiment where the protein is expressed in algae, the algae canbe, for example, green algae. For example, algae that can be usedinclude Chlorophyta such as Charoides (e.g., Charoides, Lamprothamnium,Nitellopsis, and Nitella), Zynematales (e.g., Zygnema, Closterium, andNetrium), Codials (e.g., Codium fragile, Helimida opunta, and Caulerpa),Bryopsis plumosa (e.g., Bryopsis, Pseudobryopsis, Bryopsidella,Derbesis, and Pedobesia), Acetabularia Ryukyuensis (e.g., AcetabulariaRyukyuensis, Halicoryne wrightii, Neomeris annulata, Cymopolia vanbossei, Bornettella ovalis, and Acetabularia calyculus), Siphonocladales(e.g., Valoniaceae and Boodleaceae), Cladophora (e.g., Anadyomenewritii, Cladophora, Cladophora sauteri, and Chaetomorpha), Ulva (e.g.,Ulva and Fnteromorpha), Ulotrichales (e.g., Acrosiphoniaceae,Collinsiellaceae, Monostromaceae, and Chlorocystidaceae), Prasiola,Chlorella, Chlorococcales (e.g., Pediastrum and Hydrodictyon), andVolvocales (e.g., Chlamydomonus, Pandorina, Pleodorina, and Volvox).

Exemplary algae that typically can be used in any of the embodimentsdescribed in this application include Chlamydomonas species,particularly Chlamydomonas reinhardtii, Chlorella species, and Volvoxspecies. Chlamydomonas reinhardtii, a unicellular eukaryotic green algaeis particularly advantageous. Chlamydomonas strains are available, forexample, from Chlamydomonas Genetic Stock Center, Duke University(Durham, N.C.). Auxotrophic mutants of Chlamydomonas reinhardtii(mutants that differ from the wild-type in requiring one or morenutritional supplements for growth) are readily available at theChlamydomonas Genetic Stock Center and such mutants can be geneticallycomplemented by the transforming DNA exogenous DNA introduced into thecell), which facilitates selection of algae containing a desiredtransgene. In other embodiments disabled algae can be used. Disabledalgae are genetically engineered such that they will not proliferateunless they are in very specific controlled environments (i.e., suchstrains will not grow or transfer their genes in the wild). Within thecontext of this disclosure, such algae are said to be “disabled.” Use ofsuch disabled strains inhibits or limits spread of the transgenic algaeused in the present invention into the environment.

Exemplary plants suitable for use in the methods and systems describedherein include cultured plant cells (protoplasts and callus cells) andwhole plants (single cell and multicellular plants). In variousembodiments, the plant cells (i.e., cultured plant cells or cells ofwhole plants) can be from plants including oat, wheat, rye, barley,rice, safflower, maize, legumes, such as alfalfa, soy bean, tomato,sugar beet, and potato plants. Other useful plants can be, for example,fruit-bearing plants, such as plants that bear apples, pears, cherries,grapes, citrus fruits, pineapples and bananas, and trees, such as larch.Other suitable plants include oil palms, tea, cocoa and coffee shrubs,tobacco, cotton, flax, sunflower, pasture grasses, forage cereals, feedplants, and peanut and lentil plants. Other useful plants includeArabidosis, soapworts (Saponaria), duckweed (Leminacea), ferns, mosses,and liverworts. In this embodiment, vectors commonly used in geneticengineering in plants can be used for the transfer of the nucleic acidmolecules according to the invention to plant cells.

In the methods and systems described herein the first and second nucleicacids are introduced into the cells (e.g., algal or plant cells). Inthis embodiment, the first nucleic acid encodes a promoter that iseither inducible, repressible, or both inducible and repressible, andthe second nucleic acid encodes a stability factor (e.g., Nac2 or Mbb1)that regulates the expression of a plastid mRNA. In another illustrativeembodiment, the second nucleic acid can code for a translationalactivating factor, such as, for example, Tbc2 or Tca1.

The inducible or repressible promoter controls the expression of thestability factor. In various embodiments, any suitable type of induceror repressor (e.g., a chemical or modified environmental condition) canbe used depending on the nuclear promoter being used. An exemplarypromoter suitable for use in the methods and systems described herein isthe Cyc6 promoter (see FIG. 12). Any other suitable promoters can beused including promoters with sequence similarity to the Cyc6 promotersequence, such as 60%, 70%, 80%, 85%, 90%, 95%, or 98% sequencesimilarity to the Cyc6 promoter. Also, sequences capable of hybridizingto the complement of the Cyc6 promoter under stringent hybridizationconditions can be used. Other suitable inducible or repressiblepromoters that can be used include promoters that respond to factorssuch as environmental conditions (such as anoxia, heat, drought, orlight), chemicals, nutrients, hormones, pathogens, injury, herbivory,developmental stage, and tissue type. Such promoters are known to thoseskilled in the art. Promoters may respond to more than one factor, and asingle factor may activate or repress more than one promoter.

In addition to Cyc6, other inducible promoters in Chlamydomonas includethe promoter for the CO₂-induced plasma-membrane protein gene (Genbankaccession no. U31976), the promoter for the FEA1 gene which is tightlycontrolled by iron availability (Sasaki et al., 1998; Rubinelli et al.,2002), and the promoter of the Nit1 gene that is negatively repressed inthe presence of ammonium and glutamate and induced in media lackingammonium (Fernández 1989). Examples of inducible promoters in higherplants include the light inducible promoter of the small subunit ofRubisco, the U-V inducible promoter of the chalcone synthase gene, thecoumaric-acid inducible promoter of the chalcone synthase gene, thehypoxia inducible promoter of the alcohol dehydrogenase gene, and thepathogenesis-induced promoters (PR-1-14) of tobacco, tomato, cucumber,and arabadopsis.

The stability factor is expressed under the control of the inducibleand/or repressible promoter and is introduced into the plastid where thestability factor associates, directly or indirectly (e.g., throughaccessory proteins), in the plastid with an untranslated region of anmRNA to stabilize the mRNA. In various embodiments, the untranslatedregion of the mRNA can be at the 5′ or the 3′ end of the mRNA. The mRNAis transcribed from the third nucleic acid which encodes the expressedprotein. In another illustrative embodiment, mRNA can be transcribedfrom additional nucleic acids operatively linked to the third nucleicacid or not linked to the third nucleic acid and controlled by their ownstability factors. Thus, the expressed protein is produced in theplastid under the control of the stability factor, the expression ofwhich is controlled by the inducible and/or repressible nuclearpromoter.

In one illustrative aspect, the stability factor can associate, directlyor indirectly, not only with untranslated regions of the mRNA either atthe 5′ or the 3′ end of the mRNA, or both, but the stability factor canalso associate, directly or indirectly, with coding regions of the mRNA.In another illustrative aspect, the stability factor can associatedirectly or indirectly with the mRNA, for example, by association withother accessory proteins in a complex where the other proteins associatedirectly or indirectly with the mRNA untranslated and/or coding regions.

In one embodiment, the first and second nucleic acids are incorporatedinto nuclear DNA employing, for example, integration or recombination(e.g., homologous recombination or other types of recombination). Inanother embodiment, the first and second nucleic acids are expressedusing an expression vector that is introduced into the cells. In thisembodiment, the first and second nucleic acid inserts in the vector donot recombine with nuclear DNA, but, rather, the second nucleic acid,coding for the stability factor, is expressed autonomously usingregulatory sequences present in the vector including the inducibleand/or repressible promoter coded by the first nucleic acid. Anysuitable vector known to those skilled in the art can be used includingthe vectors described herein in Examples 1-4.

In each of these embodiments, the first nucleic acid is operativelylinked to the second nucleic acid to form a recombinant nucleic acid. Anexemplary recombinant nucleic acid described herein is the Cyc6 promoter(i.e., the first nucleic acid) operatively linked to the Nac2 codingsequence (i.e., the second nucleic acid). The first and second nucleicacids can be operatively linked to each other by using cloning methodswell-known to those skilled in the art, including methods of digestingnucleic acids with restriction enzymes and ligating the first and secondnucleic acids to one another and to the ends of a digested vector, usingligases. Such cloning methods are described, for example, in Sambrook etal., “Molecular Cloning: A Laboratory Manual”, 3rd Edition, Cold SpringHarbor Laboratory Press, (2001), incorporated herein by reference, or inS. Surzycki, “Basic Techniques in Molecular Biology,” Springer-Verlag(2000), incorporated herein by reference.

In embodiments where the second nucleic acid is expressed autonomouslyunder the control of the promoter coded for by the first nucleic acid,the expression construct (i.e., the vector-insert construct) typicallycomprises a transcription terminator for terminating the transcriptionof the coding sequence present in the second nucleic acid, and cancontain other 5′ and 3′ regulatory sequences. The transcriptionterminator is typically present in the second nucleic acid, but can beincorporated into the vector.

In embodiments where the first and second nucleic acids are stablyincorporated into nuclear DNA, the transcription terminator is typicallypresent in the second nucleic acid, but can be part of the nuclear DNAsequence. The additional 5′ and 3′ regulatory sequences can be presentin the first or second nucleic acids, in the vector, and/or in nuclearDNA, such as transcriptional enhancer elements and sequences involved inmRNA stabilization. In this embodiment, the vector can also containnuclear targeting sequences that facilitate integration of therecombinant nucleic acid into nuclear DNA. In one embodiment, thenucleus can have an inoperative copy or can be missing a copy or ahomolog of the second nucleic acid.

In various embodiments described herein, the vectors for autonomousexpression of the stability factor or for incorporation of therecombinant nucleic acid into nuclear DNA have a bacterial origin ofreplication for replicating the vector construct to make large-scalepreparations of desired vectors with or without the inserted recombinantnucleic acid (i.e., the operatively linked first and second nucleicacids) for use in cloning. The vectors also typically have restrictionendonuclease cleavage sites for the insertion of DNA fragments (e.g., amultiple cloning site), and selectable genetic markers for the selectionof transformants. The selectable marker can be a marker, such as theaadA gene or nptII, which allows for growth of the transformed cells onmedia supplemented with antibiotics (Goldschmidt-Clermont, Nucl. AcidsRes., vol. 19, pages 4083-4089 (1991)). Both native gene (arg7, nit1)and foreign gene (ble, aphVIII, aadA, nptII) selectable markers havebeen developed as reporter genes for nuclear transformation.

The vectors with the recombinant nucleic acid (i.e., an insertcomprising the first and second nucleic acids) are introduced into thecells (e.g., algal or plant cells) by standard transformation techniqueswell-known to those skilled in the art. Exemplary transformation methodsinclude electroporation, glass-bead mediated DNA delivery, the use ofpolyethylene glycol-mediated transformation, biolistics, and the like.

In one embodiment, for transforming algae, autolysin, an enzyme which isreleased during mating and degrades cell walls is used to break down thecell wall before transformation. In an alternate embodiment, mutantstrains which lack the ability to synthesis the cell wall (e.g.,cw15cw10) have been generated and can be used for efficienttransformation.

In one illustrative aspect, transformants can be detected by PCR andSouthern blotting. Other procedures known to those skilled in the artcan also be used, such as for example, antibiotic addition, copperaddition, antibody detection (e.g., ELISA and Western blotting), andsequencing. The choice of such procedure depends upon the constructused.

If a transgene is to be expressed in the plastid, the third nucleic acidcan be incorporated into a vector and the vector constructs can be madeand can be replicated generally as discussed above for the first andsecond nucleic acids. Illustratively, plastid transformation can beachieved with biolistics, in which the vector containing the transgeneis introduced into the cell on a gold or tungsten microparticleaccelerated by an inert gas, such as helium. This method may cause lessdamage to the cells. In a related illustrative embodiment, the cells tobe transformed can be plated on selective solid agar media andDNA-coated tungsten beads can be delivered into the plastid byaccelerating them with helium gas or gun powder. Using this technique,efficient delivery of recombinant DNA into the plastid can be achieved.

In one embodiment, detection of integration of the third nucleic acidinto plastid DNA can rely on expression of heterologous DNA encoding thebacterial aminoglycoside adenyl transferase gene (aadA). This embodimentenables a method of selecting transformants using the antibioticspectinomycin or streptomycin. Using this reporter construct, it ispossible to specifically insert, disrupt, modify, mutate or delete anynon-essential gene or cis acting elements in the plastid.

In another illustrative embodiment, chloroplast transformation with atransgene can be achieved using a transgene flanked by homologouschloroplast targeting sequences that facilitate integration of thetransgene into the chloroplast DNA. In one embodiment, integration ofthe transgene can occur by two homologous recombination events betweenthe flanking chloroplast sequences of the vector and their homologoussequences in the chloroplast genome. In one embodiment, the chloroplastcan have an inoperative copy or can be missing a copy or a homolog ofthe third nucleic acid.

Exemplary modifications of nucleic acids that make the nucleic acidsforeign include, but are not limited to, modifying the nucleic acids toachieve codon optimization, ligating the nucleic acids to 5′ or 3′untranslated regions of other genes, adding promoter or terminationsequences to nucleic acids, ligating sequences useful for homologousrecombination, and adding other elements required for gene expression,targeting, or stabilization, for example, to the nucleic acids.Additional modifications include fusing the nucleic acid to the nucleicacid of other native or transgenes to form a fusion protein.

Exemplary schematic outlines of plastid gene regulation systems that arewithin the scope of this invention are shown in FIGS. 2-5. FIG. 1 showsa schematic outline of a plastid gene regulation system in which thenuclear inducible promoter is induced in the presence of an inducer. Inthis embodiment, the inducer (e.g., an environmental condition such aslow oxygen levels) induces the promoter that regulates expression of thestability factor and the stability factor is expressed. Followingtranslation, the stability factor is targeted to the plastid where itassociates with a specific mRNA, depending on the stability factor beingexpressed, and the mRNA and the protein it encodes are expressed.

FIG. 3 shows a schematic outline of an exemplary plastid gene regulationsystem in which the nuclear inducible promoter is repressed in theabsence of an inducer. In this embodiment, the absence of the inducer,the inducible promoter is not activated and the stability factor is notexpressed. Without the stability factor, the mRNA in the plastid isdegraded or not translated and the protein is not expressed.

FIG. 4 shows a schematic outline of an exemplary plastid gene regulationsystem in which the nuclear repressible promoter is repressed in thepresence of a repressor (e.g., a predetermined level of copper in themedium). In this embodiment, in the presence of the repressor, therepressible promoter is not activated and the stability factor is notexpressed. Without the stability factor, the mRNA in the plastid isdegraded or not translated and the protein is not expressed.

FIG. 5 shows a schematic outline of an exemplary plastid gene regulationsystem in which the nuclear repressible promoter is induced in theabsence a repressor (e.g., a reduced level of copper in the medium orthe absence of copper in the medium). In this embodiment, in the absenceof the repressor the nuclear promoter that regulates expression of thestability factor is induced and the stability factor is expressed.Following translation, the stability factor is targeted to the plastidwhere it associates with a specific mRNA, depending on the stabilityfactor being expressed, and the mRNA and the protein it encodes areexpressed.

In embodiments where it is desirable to isolate and purify the expressedproteins obtained using the methods and systems described herein, theproteins can be expressed and then purified using conventionaltechniques. For example, the proteins can be obtained in a form that isabout 40% pure, about 50% pure, about 60% pure, about 70-80% pure, about90% pure, about 95% pure, or about 98% pure. For purification from thecells, a lysate can, for example, be subjected to ammonium sulfateprecipitation followed by DEAE-Sepharose column chromatography. Otherconventional techniques known to those skilled in the art can be usedsuch as gel filtration, ion exchange chromatography, DEAE-Sepharosecolumn chromatography, affinity chromatography (such as using theFLAG-tagged system described in Example 2 below), solvent-solventextraction, ultrafiltration, and HPLC. Alternatively, purification stepsmay not be required because the proteins may be present in such highconcentrations that the protein is essentially pure in the lysate (e.g.,70-80% pure). The expressed protein can be concentrated by suchtechniques as, for example, ultrafiltration and tangential flowfiltration.

In one embodiment, the cells can be lysed, for example, by sonication,heat, or chemical treatment, and the homogenate centrifuged to removecell debris. The supernatant can then be subjected to ammonium sulfateprecipitation, and additional fractionation techniques as required, suchas gel filtration, ion exchange chromatography, DEAE-Sepharose columnchromatography, affinity chromatography, solvent-solvent extraction,ultrafiltration, and HPLC to purify the expressed protein. It should beunderstood that the purification methods described above forpurification of the expressed proteins from the culture medium or fromcells are nonlimiting and any purification techniques known to thoseskilled in the art can be used to purify the expressed proteins if suchtechniques are required to obtain a substantially pure protein.

The cells (e.g., algal or plant cells) can be cultured using a varietyof techniques to promote protein expression. Culture media for cells,including algal and plant cells, are known in the art and are typicallysupplemented with a carbon source (e.g., glucose or acetate). The cellscan be cultured to maintain a desired density, for example, as describedbelow using a culture system and device useful for the production ofhydrogen gas as an example.

As discussed in detail above, the expression methods and systemsdescribed herein may be used to produce hydrogen. Thus, in anotherembodiment an apparatus for the production of hydrogen is provided. Theapparatus comprises a first vessel configured to hold a cell culture ina substantially oxygen-depleted environment, a first pump in fluidcommunication with the first vessel and configured to pump a medium intothe first vessel at a predetermined rate, and a measuring device coupledto the first vessel and configured to measure an amount of hydrogenproduced by the cell culture.

FIG. 7 illustrates an apparatus 10 for producing hydrogen that may beused in some embodiments. The apparatus 10 includes a fresh mediumstorage vessel 12, a pump 14, a reaction system 16, and an overflowvessel 18. The fresh medium storage vessel 12 may be embodied as anytype of vessel capable of storing an amount of medium, such as TAP(acetate) or HSM (minimal), in a substantially hermetically-sealedenvironment. In some embodiments, an amount of gas 24, such as argongas, is pumped into the fresh medium storage vessel 12 via a conduit 26to purge the vessel 12 of oxygen to thereby form a substantiallyoxygen-depleted environment therein. The conduit 26 may be embodied asany type of tube, line, or other conduit capable of facilitating passageof a fluid (e.g., a gas) into the fresh medium storage vessel.

The pump 14 is fluidly coupled to the fresh medium storage vessel 12 viaa conduit 28 and to the reaction system 16 via a conduit 30. The conduit28 (and the conduit 26 if included) is coupled to the vessel 12 suchthat the substantially hermetically-seal environment of the fresh mediumstorage vessel 12 is maintained. The conduits 28, 30 may be embodied asany type of tubes, lines, or other conduits capable of facilitatingpassage of a fluid via a pumping action provided by the pump 14. Thepump 14 may be embodied as any type of pump capable of pumping an amountof medium from the fresh medium storage vessel 12 to the reaction system16 at a predetermined rate without adversely interacting with the freshmedium. For example, in one particular embodiment, the pump 14 isembodied as a peristaltic pump such that the potential for damage to themedium during the pumping process is reduced.

The reaction system 16 includes a reaction vessel 20 and an agitationdevice 22. The reaction vessel 20 is substantially similar to freshmedium storage vessel 12 and may be embodied as any type of vesselcapable of storing an amount of medium and algae culture, or other typeof host cell, in a substantially hermetically-sealed environment. Freshmedium is pumped from the fresh medium storage vessel 12 to the reactionvessel 16 via the conduits 28, 30 and the pump 14. Because the freshmedium is stored in a substantially oxygen-depleted environment, thelikelihood of inadvertently introducing oxygen into the reaction vessel16 is reduced. The conduit 30 is coupled to the reaction vessel 20 suchthat the substantially hermetically-sealed environment of the reactionvessel 12 is maintained.

The agitation device 22 is operably coupled to the reaction vessel 20and may be embodied as any type of device capable of maintaining theculture stored in the reaction vessel 20 in an agitated state. Forexample, the agitation device 22 may be embodied as an automatedstirring device such as a magnetic stir bar assembly or the like.

A conduit 32 drains any overflow of culture from the reaction vessel 20to an overflow vessel 18. The overflow vessel 18 may be substantiallysimilar to vessels 12, 20 and may be embodied as any type of vesselcapable of storing an amount of culture therein. The conduit 32 issubstantially similar to conduits 28, 30 and may be embodied as any typeof tube, line, or other conduit capable of facilitating passage of afluid from the reaction vessel 20 to the overflow vessel 18. Similar toconduit 30, the conduit 28 is coupled to the reaction vessel 20, suchthe that substantially hermetically-sealed environment of the reactionvessel 20 is maintained. The conduit 30 may be coupled to the reactionvessel 20 in a position such that the level of culture contained in thereaction vessel 20 remains at (or within) a predetermined level(s) byexpelling a portion of the culture into the overflow vessel 18.

In some embodiments, a measuring device 34 may be coupled to thereaction vessel 20 via a communication link 36 such that the amount ofhydrogen or other gas produced by the culture in the vessel 20 may bemeasured. The measuring device 34 may be embodied as any type of devicecapable of measuring an amount of the gas of interest. In one particularembodiment, the measuring device 34 is embodied as a mass spectrometer,but in other embodiments, other types of measuring devices may be used.The communication link 36 may be any type of communication link capableof facilitating the communication of data to the measuring device 24such as, for examples, any number of wires, cables, fiber optic cables,tubes, conduits, or the like. In one particular embodiment, thecommunication link 36 includes an electrode portion positioned in thereaction vessel 20. The electrode portion may be, for example, a silverelectrode.

In some embodiments, the apparatus 10 may include a filter system 40 anda secondary pump 38. The filter system 40 is coupled to the overflowvessel 18 via a conduit 42 and to the pump 38 via a conduit 44. The pump38 is coupled to the fresh medium storage vessel 12 via a conduit 46.The conduits 42, 44, 46 are substantially similar to conduits 28, 30, 32and may be embodied as any type of tube, line, or other conduit capableof facilitating passage of a fluid. The pump 38 may be similar to thepump 14 and may be embodied as any type of pump capable of pumping anamount of “spent” culture from the overflow storage vessel 18 to thereaction fresh medium storage vessel 12 at a predetermined rate withoutadversely interacting with the fresh medium. For example, in oneparticular embodiment, the pump 38 is embodied as a peristaltic pump.The filter system 40 may be embodied as any number and type of filtersand associated interconnects that are capable of filtering the culturestored in the overflow vessel 18.

In operation, the pump 14 is configured to pump fresh medium from thefresh medium storage vessel 12 to the reaction vessel 20 of the reactionsystem 16 at a predetermined rate. In one particular embodiment, thepump 14 is configured to pump the fresh medium into the reaction vessel20 at a rate substantially equal to a rate of cell growth of an algaestored in the reaction vessel 20. As discussed in detail above, becausethe algae, or other host cell type, is stored in the reaction vessel 20in a substantially oxygen-depleted environment desirable gene expressionis induced in the algae, or other host cell type, such that hydrogenproduction is increased. The substantially oxygen-depleted environmentof the reaction vessel 20 is maintained while introducing fresh mediumfrom the fresh medium storage vessel 12 because such fresh medium isalso stored in a substantially oxygen-depleted environment in the vessel12 as discussed above. Alternatively, in other embodiments, the algae,or other host cell type, stored in the reaction vessel 20 may beself-induced. Regardless, it should be appreciated that apparatus 10 isa single phase apparatus. That is, the algae, or another host cell type,stored in the reaction vessel 20 proliferate and are induced in the samevessel.

As fresh medium is introduced into the reaction vessel 20, the agitationdevice 22 is configured to keep the culture stored in the reactionvessel in a continual state of agitation. In addition, as fresh mediumis introduced, a portion of the existing culture is removed from thereaction vessel to the overflow vessel 18. In this way, the amount ofalgae, or another host cell type, contained in the reaction vessel 20 ismaintained at a substantially constant value. In embodiments includingthe pump 38 and the filter system 40, the pump 38 removes an amount of“spent” culture from the overflow vessel and reintroduces such mediuminto the fresh medium storage vessel after being filtered by the filtersystem 40 to remove any algae, or other host cell type, containedtherein.

Referring now to FIG. 8, in one particular embodiment, an apparatus 50for producing hydrogen includes a fresh medium storage vessel 52, aperistaltic pump 54, a reaction system 56, and an overflow vessel 62.The fresh medium storage vessel 52 is substantially similar to the freshmedium storage vessel 12 and is illustratively embodied as a 0.25 litervessel. An amount of fresh medium 64, illustratively embodied as TAP(acetate) or HSM (minimal), is stored in the vessel 52. A cap 66 iscoupled to the vessel 52 such that an inner cavity 68 of the vessel 52is substantially hermetically-sealed from the outside environment. Aconduit 70 is coupled to the cap 66 and includes an end portion 72positioned in the inner cavity 68 of the vessel 52. An amount of argongas 74 is introduced into the inner cavity 68 via the conduit 70 tothereby substantially purge the inner cavity of oxygen.

The peristaltic pump 54 is coupled to the fresh medium storage vessel 52via a conduit 76 and to the reaction system 56 via a conduit 78. Theperistaltic pump 54 is illustratively embodied as a model IP4peristaltic pump, which is commercially available from Ismatec ofGlattburg, Switzerland. The pump 54 is configured to pump an amount offresh medium from the fresh medium storage vessel 52 to the reactionsystem 56 at a predetermined rate substantially equal to the growth rateof an algae culture, or another host cell type, stored in the reactionsystem 56.

The reaction system 56 includes a reaction vessel 88, illustrativelyembodied as a 0.25 liter vessel, and a magnetic stir bar system 90configured to continually agitate an amount of medium and algae culture94, or another host cell type, stored in the reaction vessel 88. Themagnetic stir bar system 90 is illustratively embodied as a model KM02magnetic stir bar, which is commercially available from Milian ofGeneva, Switzerland. A cap 92 is coupled to the reaction vessel 88 suchthat an inner cavity 94 of the vessel 88 is substantiallyhermetically-sealed from the outside environment. The conduit 78 iscoupled to the cap 92 and includes an end portion 96 positioned in theinner cavity 94 of the reaction vessel 88.

A mass spectrometer 100 is also coupled to the reaction vessel 88 via acommunication link 102. The mass spectrometer 100 is illustrativelyembodied as a model MM8-80 mass spectrometer, which is commerciallyavailable from VG Instruments of Cheshire, United Kingdom. Thecommunication link 102 includes an electrode 104 positioned in the innercavity 94 of the vessel 88. The mass spectrometer 100 is configured tomeasure the amount of hydrogen (and, in some embodiments, the amount ofoxygen) produced by the medium and algal culture, or another host celltype, stored in the reaction vessel 88.

Additionally, a conduit 106 is coupled to the cap 92 and includes an endportion 108 positioned in the inner cavity 94 of the vessel 88. A distalend 110 of the conduit 106 is positioned in an inner cavity of theoverflow vessel 62. The conduit 106 is so positioned such that an amountof medium and algal culture, or another host cell type, is removed fromthe reaction vessel 88 at a rate substantially equal to a rate of cellgrowth of the algae, or another host cell type, stored in the reactionvessel 88.

The description above applies to all of the methods and systemsdescribed herein. The following examples are for purposes ofillustration only and are not intended to limit the scope of theinvention as defined in the claims which are appended hereto. Thereferences cited in this document are specifically incorporated hereinby reference.

EXAMPLE 1 Inducible Plastid Expression System for a Native Gene

A vector containing the Nac2 gene under the control of the Cyc6 promoterwas constructed using molecular cloning techniques known to thoseskilled in the art. Cloning methods are described, for example, inSambrook et al., “Molecular Cloning: A Laboratory Manual”, 3rd Edition,Cold Spring Harbor

Laboratory Press, (2001), incorporated herein by reference or in S.Surzycki, “Basic Techniques in Molecular Biology,” Springer-Verlag(2000), incorporated herein by reference.

To place the Nac2 gene under the control of the Cyc6 promoter element, achimeric DNA fragment comprising the Cyc6 promoter fused to the codingsequence of psbD was generated by overlap-extension PCR using 4oligonucleotides specific for the Cyc6 promoter element and Nac2 genomicDNA. The resulting PCR fragment consisted of a 428 base-pair fragment ofCyc6 promoter sequence fused in frame with an 833 base-pair fragment ofNac2 genomic sequence. The PCR fragment was sub-cloned and sequenced.The PCR fragment was then cloned into the pNac2(midi) plasmid using theunique restriction sites XbaI and AatII. The pNac2(midi) plasmidcontains a 5.1 kb chimeric midi-gene of Nac2 which has been previouslydescribed by Boudreau et al. (2000), incorporated herein by reference.The gene is composed of the 5′ genomic sequence of Nac2 fused to the 3′cDNA sequence and results in an open reading frame (ORF) encoding theentire Nac2 protein which is tagged with a triple HA epitope at theC-terminal end of the protein. The pNac2(midi) was digested with XbaIand AatII. The PCR fragment was then ligated directionally into theplasmid. The resulting plasmid pcy6Nac2(midi) contains a 428 basepairfragment of Cyc6 promoter sequence fused in frame with the Nac2 midigene.

Finally, the 5.8 kb cyc6Nac2transgene was cloned into the pSL17 plasmidusing the unique restriction sites in the multiple cloning site of pSL17(i.e., EcoRI and XbaI; see FIG. 9). pSL17 contains the aphVII cassetteconferring resistance to the antibiotic paromomycin and a multiplecloning site for cloning. The resulting 10.8 kb plasmid, pcy6Nac2(paroR)(see FIG. 10), was used to transform nac2-26 mutant cells. Sequences forNac2 and Cyc6 used in the construction of the vector are provided inFIGS. 11 and 12, respectively.

The pcy6Nac2(paroR) vector was introduced into a nac2 null mutant,nac2-26 by electroporation. Algal and plant transformation methods areknown to those skilled in the art and are described, for example, inSambrook et al., “Molecular Cloning: A Laboratory Manual”, 3rd Edition,Cold Spring Harbor Laboratory Press, (2001), incorporated herein byreference.

To isolate a transgenic Chlamydomonas strain containing a Cyc6 inducibleNac2 gene, nac2-26 cells were first treated with autolysin and thentransformed by electroporation using pcyc6Nac2(paroR). The resultingtransformants were plated on TAP medium supplemented with the antibioticparomomycin (20 μg/ml). Paromomycin resistant colonies were screened forthe ability to grow photo-autotrophically on minimal medium supplementedwith 150 μM Nickel(II), (an inducer of Cyc6 transcription) and minimalmedium lacking copper (HSM-Cu⁺²; see FIG. 13). Photo-autotrophic strainswere then tested for the ability/inability to grow on minimal mediumlacking the inducer (HSM).

Using this regimen, the transgenic strain cy6Nac2.49 was isolated (seeFIG. 13). This strain was capable of growing photoautrophically onHSM-Cu⁺² but, was unable to grow phototrophically on HSM supplementedwith copper. The resulting strain, cy6Nac2.49, grows in two waysincluding 1.) photo-autotrophically in medium lacking copper or 2.) inanaerobically grown cultures when oxygen and copper are present in thegrowth medium where the cells lack PSII complexes (see FIG. 1). Thus, inthe transgenic strain, cy6Nac2.49, the production of photosyntheticoxygen is controlled through a nuclear promoter, which responds tohypoxia.

Furthermore, sealed cultures of cy6Nac2.49 grown under non-inducingconditions will quickly become anaerobic, because photosynthetic oxygenis not released but oxygen consumption by mitochondrial respirationremains constant. In sealed cultures of cy6Nac2.49, a feedbackinhibition loop exists where hypoxia induces photosynthetic oxygenproduction, which then re-represses PSII synthesis and photosyntheticoxygen evolution.

In fact, this is exactly what was observed when sealed illuminatedcultures of cy6Nac2.49 were grown in complete medium. Initially, theoxygen content of the culture was present at atmospheric levels, andthen it was quickly consumed, resulting in anaerobis and induction ofhydrogen evolution. After a period of anaerobic growth, oxygen returnedto the culture at 2 times the atmospheric levels inside the vessel,inhibiting hydrogen evolution (data not shown). In a conventional sealedvessel, only one cycle of oxygen consumption and hydrogen production wasobserved, possibly because the consumption of oxygen ceased when thereduced carbon was consumed by mitochondrial respiration whilephotosynthetic oxygen production remained constant.

Wild-type, nac2-26 (the parental strain of cy6Nac2.49) and, cy6Nac2.49cells were tested for their ability to grow on complete (TAP) medium,complete medium supplemented with the antibiotic paromomycin (TAP+Paro),minimal medium (HSM), and minimal medium lacking copper (HSM-Cu⁺²) (FIG.10). Western blot analysis performed on whole cell extracts of wild-typeand cy6Nac2.49 cells grown in non-inducing (TAP) and inducing conditions(TAP-Cu⁺² and TAP-O₂) is shown in FIG. 14. Western blots were probedwith antibody recognizing α-HydA as a control for anaerobiosis, α-D2 andα-RbcL.

FIG. 15 shows the result of an experiment to measure hydrogen evolution.Cy6Nac2.49 cells were sealed in an illuminated vessel where dissolvedgas in the culture medium could be measured using a mass spectrometer(oxygen-dashed line, hydrogen-solid line), then shifted from inducing tonon-inducing conditions through the addition of copper to the growthmedium (TAP-Cu⁺² to TAP). The concentration of H₂ was measured in theliquid phase and is indicated in mBar.

Conventional sealed vessels are not adequate to sustain hydrogenproduction using the transgenic strain cy6Nac2.49, so a sealed, anoxicsystem was designed to provide fresh, oxygen-depleted medium at aconstant rate to a growing cy6Nac2.49 culture, to maintain it inexponential growth phase (see FIGS. 7 and 8). It was hypothesized thatmaintaining a culture in an exponential growth phase would result in theestablishment of a cycle of oxygen consumption/hydrogenproduction/oxygen production. When cells of cy6Nac2.49 were grown inthis system, we observed an induction of hydrogen evolution shortlyafter the onset of hypoxia to the culture. Synthesis of PSII complexeswas then induced along with a slight rise in oxygen in the vessel.Unlike the conventional sealed vessels, the photosynthetic oxygenreleased does not inhibit hydrogen production, presumably becausephotosynthetic oxygen production never exceeds the consumption of oxygenby mitochondrial respiration. In this system, the production of hydrogenis directly linked to light energy and therefore represents a directbiophotolysis method for the production of hydrogen. Using the anoxicsystem, we achieved a constant rate of hydrogen evolution reachingapproximately 0.5% of the gas phase.

Oxygen is evolved as a byproduct of photosynthesis. As a result, acentral challenge to sustaining algal hydrogen evolution using lightenergy (a process sometimes known as biophotolysis) has been to overcomeoxygen sensitivity of the hydrogenase enzyme. In contrast to the directbiophotolysis method developed by these inventors, indirectbiophotolysis methods (or two-stage photosynthesis and hydrogenproduction) apply spatial or/and temporal separation of thephotosynthetic oxygen and hydrogen production to overcome theoxygen-sensitivity of the hydrogenase enzyme (Benemann 1996; Melis2000). The first stage involves normal oxygenic photosynthesis: therelease of oxygen, fixation of CO₂, and accumulation of biomass. In thesecond phase, oxygenic photosynthesis is inhibited physiologicallythrough the depletion of an important nutrient such as sulfur. Becauserates of oxygenic photosynthesis decline drastically after about 22hours of sulfur starvation, sealed cultures become anaerobic owing tothe net consumption of oxygen caused by mitochondrial respiration (Melis2000). Once anaerobia is established, the hydrogenase pathway is inducedand hydrogen is evolved using electrons derived primarily from theremaining photo-oxidation of water, but also from the catabolism ofendogenous substrates such as protein and starch (Ghirardi 2000).

The differences between the anoxic system, a direct biophotolysismethod, and indirect biophotolysis methods reveals several importantadvantages for the use of the anoxic system. First, inherent to theanoxic system, there is a 50% gain in capacity for hydrogen productionsimply because oxygen and hydrogen production occur in a singleilluminated sealed vessel. The two-stage photosynthesis and hydrogenproduction method or indirect biophotolysis implies the temporal and/orspatial separation of the oxygen and hydrogen production phases and as aresult, requires two vessels with one of the vessels not being usedduring hydrogen production with a loss of 50% of capacity forproduction. Secondly, two-stage photosynthesis and hydrogen productionmethods rely on physiological depletion of sulfur to inhibit oxygenicphotosynthesis. Severe sulfur starvation has a wide range of effects ona variety of cellular processes. The hydrogenase enzyme that catalyzesthe release of hydrogen contains Fe—S clusters, assembly of which isrequired for its function (Posewitz, et al. (2004)). In addition, sulfurdepletion negatively affects other important chloroplast complexesimportant to hydrogen evolution like PSI. Clearly, physiologicaldepletion of sulfur severely affects important parts of the hydrogenevolution machinery. In contrast, the anoxic system does not rely ondepletion of an important micronutrient to induce hydrogen production.In fact, hydrogen production occurs under optimum physiologicalconditions (in an exponentially growing culture in complete medium).

Finally, a major hurdle in the large-scale production of hydrogen using,for example, algae is providing light-energy to large dense cultures. Inlarge dense cultures of algae, large quantities of chlorophyll in thelight-harvesting complexes can prevent light energy from reaching cellsat the center of the vessel. In our direct biophotolysis method,hydrogen production occurs in a system, where an optimum cell densitycan be established for maximum light absorption and hydrogen production.

EXAMPLE 2 Inducible Plastid Expression System for a Foreign Gene

Chloroplast transformation vector. The plasmid pSK108 contains a 3 kbfragment of chloroplast DNA which includes the psbD gene and 5′ flankingsequences to direct it to the region surrounding the psbD gene (FIG.16). The construct also contains the aadA cassette inserted upstream ofthe psbD gene. A transgene can be inserted in frame using the NcoI andSphI sites of pSK108. Once ligated, the new vector would contain thetransgene (plus 3 bps) with the 5′ end of atpA driving its expressionand the 3′ sequence of rbcL acting as a terminator. The atpA promoterdrives the expression of a gene encoding the ATP-generating proton pumpof the chloroplast, and, thus, is not subject to the D1 repairmechanism.

Three FLAG-tagged foreign genes wVP28, DILP, and IBVD were individuallysubcloned into the chloroplast transformation and expression vectorpCG12 (FIG. 17). The vector integrates downstream of the atpBchloroplast locus. The transgenes are driven by the atpA promoter andcarry the stability factor association site of the 5′ UTR of psbD (FIGS.18 and 19).

These vectors were co-transformed with the p228 vector, which carriesthe 16S rRNA gene of Chlamydomonas and confers resistance tospectinomycin, into the cyc6/Nac2 inducible strain (Cyc6 promoter as thecontrol promoter and Nac2 as the stability factor).

EXAMPLE 3 Overexpression of the HydA1, HydEF, and HydG Genes in C.reinhardtii Chloroplasts

Whether hydrogenases can be overexpressed in C. reinhardtii and whetherthis leads to enhanced hydrogen production will be tested. Recentexperiments have shown that coexpression of HydEF, HydG and HydA1 in E.coli is sufficient for producing active Fe hydrogenase (Posewitz, et al,(2004)). Overexpression of proteins in the nuclear compartment of C.reinhardtii has met with little success mostly because transgenes areoften silenced. Therefore, these genes will be expressed in thechloroplast compartment using biolistic transformation. There areseveral advantages for using this strategy. First, gene silencing doesnot occur in the chloroplast. Second, each plastid gene is present in 80copies in C. reinhardtii. Third, recent experiments have shown that itis indeed possible to achieve high expression levels of foreign proteinsin the chloroplast if these genes are driven by chloroplast promoters,5′ and 3′ UTRs, and if the coding sequence is resynthesized using biasedchloroplast codon usage (Mayfield, et al. (2001)). There is a strong ATbias for chloroplast genes.

Each of the coding sequences of HydA1, HydEF and HydG will first bereconstructed taking into account the chloroplast codon usage of C.reinhardtii. This will be achieved by using published methods which havebeen used successfully for synthesizing foreign genes for expression inthe chloroplast. As an example, we have recently successfullyoverexpressed two viral proteins in the chloroplast of C. reinhardtii(see below). The transgene will be inserted in the chloroplast invertedrepeat so as to increase its copy number twofold. As a host strain, thecyc6Nac2 strain will be used. This strain contains the nuclear nac2mutation and the Nac2 gene driven by the Cyc6 promoter which is inducedby copper depletion or anaerobic conditions.

At this time it is not known which protein among the HydA1p, HydEFp andHydGp proteins is limiting for hydrogen production. To test this, eachof the three genes fused to the psbD promoter and 5′ UTR will first beinserted individually within the chloroplast inverted repeat usingbiolistic transformation for overexpression. One possibility is toinsert the gene in the ribosomal operon within the spacer between the16S and 23S rRNA genes, a strategy which has been used successfully forhigh expression in the chloroplasts of higher plants. Because thetransgene is under control of the psbD 5′ UTR which is driven via Nac2by the Cyc6 promoter, the transgene will only be expressed underanaerobic conditions. Expression will be monitored by RNA blothybridizations or real time RT-PCR. For each of the three genes tested,hydrogen production will be assayed by growing the transformed cells ina closed bottle connected with a tubing to an upside-down burette filledwith water and by measuring the volume of the gas directly from thevolume of water that is displaced as described by Zhang and Melis(2002). If hydrogen production is increased relative to the cyc6Nac2control, this will indicate that the overexpressed protein is limiting.If these experiments reveal that more than one of these proteins islimiting for hydrogen production, both proteins will be expressed usingthe same strategy. It is possible that expression of these threeproteins is adjusted in wild-type cells so that each protein needs to beoverexpressed to increase the yield of hydrogen production. In this caseoverexpresson of the three proteins will be required. Expression ofmultiple transgenes has been achieved in higher plant chloroplasts(Quesada-Vargas, et al. (2005)). If expression with the psbD 5′UTR isnot sufficient, other strong chloroplast promoters-5′UTRs such as psbA,atpA and the ribosomal promoter will be tested.

EXAMPLE 4 Expression of Genes that Affect Hydrogen Production

In addition to the above, several other genes will be tested forincreased hydrogen production using the inducible and/or repressiblesystem for the expression of proteins in plastids. Two examples areoxygen-insensitive hydrogenases or reducing antenna size (Melias, et al.(2004); Ghirardi, et al. (2005)). Briefly, the former involves cloningand characterizing native and mutagenized hydrogenase genes fromChlamydomonas and other organisms for reduced sensitivity to oxygen. Theobjective of the latter, antenna reduction, is to reduce the amount ofphotons captured by algal cells, so that light may penetrate deeper intophotoreactors, thus becoming available for use by normally shaded cells.Algal cells are very effective at capturing but not utilizing light,wasting as much as 80% of absorbed photons. Genes that regulate antennasize have been identified through DNA insertional mutagenesis. The PSIIand PSI antenna size of mutant, tla1, was 50% and 65% of the wild typestrain. Finally, mutants strains have been identified with presumablyincreased rates of respiration that consequently lower the levels ofoxygen available for inhibiting hydrogenases (Krause, et al. (2005)).The genes will be inserted into the cy6Nac2.49 transgenic strain andevaluated for their contribution to increasing hydrogen production ofthe strain.

One important limiting factor for hydrogen production is the competitionwith the Calvin-Benson cycle. One possibility to enhance electron flowto the hydrogenase is to decrease the activity of the Calvin-Bensoncycle by decreasing the amount of an enzyme which participates in thiscycle. For example, phosphoribulose kinase (PRK) could be utilizedbecause two mutants of Chlamydomonas, F60 and ac214, deficient in PRKactivity are available. The PRK gene will be fused to the inducible Cyc6promoter and this construct will be inserted into F60. The advantage ofthis strategy is that PSII and the Calvin-Benson cycle will beoperational together in the absence of copper (or oxygen) thus allowingfor storage of reducing power. Both genes will be shut off in thepresence of copper (or oxygen). Thus, under conditions in whichhydrogenase is induced, electron flow will be diverted from theCalvin-Benson cycle to the hydrogenase and hydrogen production will beenhanced.

In another illustrative embodiment, PRK temperature-sensitive mutantswill be screened for. In this way the Calvin-Benson cycle can be shutoff at the restrictive temperature and electrons diverted to thehydrogenase. The PRK mutants will be transformed with a library ofmutagenized PRK genes generated by PCR. Transformants will be selectedon minimal medium at the permissive temperature (24° C.). Colonies willbe replica-plated to minimal medium and will be grown at the restrictivetemperature (32° C.) and mutants unable to grow will be identified. Toverify that the PRK gene carries a mutation, the gene will be amplifiedby PCR and sequenced. It will also be possible to screen the mutants byfluorescence since a block in the Calvin-cycle is likely to increase thefluorescence yield of these mutants.

In another embodiment, cyclic electron flow represents another route ofdiversion of electrons from the hydrogenase, and we will use mutantsdeficient in state transitions that are blocked in state 1. Statetransitions involve a rebalancing of the light excitation energy betweenthe antenna of PSII (LHCII) and PSI through a reversible displacement ofthe mobile part of LHCII from PSII to PSI under changing lightconditions which allows for an optimal photosynthetic yield. In state 1,the mobile part of LHCII is associated with PSII, whereas in state 2 itis associated with PSI. Moreover, in Chlamydomonas, state 1 favorsmostly linear electron flow while state 2 leads to cyclic electron flow(Finazzi et al., 2002). Thus, there is no cyclic electron flow inmutants blocked in state 1. The stt7 mutant which is known to be blockedin state 1 (Depège et al., 2003) will be crossed with nac2-26 containingthe Cyc6-Nac2 and Cyc6-PRK construct and it will be determined whetherthis leads to improved hydrogen production when PSII activity isrepressed. Alternatively, once the temperature-sensitive PRK mutants areavailable, the mutations will be crossed to the nac2-26 stt7 Cyc6-Nac2strain. These strains will be tested for hydrogen production under theconditions described above.

Other mutants besides stt7 deficient in state transitions will beanalyzed. The analysis of these mutants is of particular interestbecause alterations in state transitions can be caused indirectly byalterations in the regulation of photosynthetic and mitochondrialelectron flow which may change the ratio of mitochondrial respirationrelative to photosynthetic oxygen evolution. Mutants of this sort havealready been reported to have increased hydrogen production incomparison to WT cells (Kruse et al., 2005).

EXAMPLE 5 Inducible Plastid Expression System for Foreign Genes

The selectable marker gene, aadA, was used for inducible chloroplastgene expression. It can be expressed in a Nac2-dependent fashion, can beeasily screened using the antibiotic spectinomycin, and it is known tohave a high specific activity. Even low aadA expression results in someantibiotic resistance, and therefore provides a measure for the“tightness” of cy6Nac2 regulation in Ind41_(—)18 (described below). Achloroplast integration vector had been constructed that carries thepromoter and 5′UTR of psbD driving the expression of the aadA gene.

The nac2-26 mutant strain was previously described (Kuchka, et al. EMBOJ. 7, 319-324; Nickelsen, et al. EMBO J. 13, 3182-3191). The cyc6Nac2.49strain contains a trans-gene consisting of the Cyc6 promoter fused tothe Nac2 midi-gene inserted into the nuclear genome of the nac2-26mutant (Δnac2::cy6proNac2). Ind41 was derived from cy6Nac2.49 byreplacing the psbD promoter and 5′UTR with a 675 fragment containing thepetA promoter and 5′UTR (Δnac2::cy6pro Nac2::5′petA-psbD). Ind41-18 isrelated to the Ind41 strain, except that the aadA cassette in theInd41-18 strain has been completely excised from the chloroplast DNA andthe strain is therefore sensitive to spectinomycin(Δnac2::cy6proNac2::5′petA-psbD[Spc^(S)]). Ind_aadA_(—)117 was derivedfrom Ind41-18 and contains the aadA cassette driven by the psbD promoterand 5′UTR inserted downstream of the atpB gene(Δnac2::cy6proNac2::5′petA-psbD::5′psbD-aadA).

Screening for Ind_aadA Transgenic Strains

Integration of the 5′ psbD-aadA cassette into the chloroplast genome ofInd41_(—)18 cells was accomplished through biolistic transformation ofcopper-starved Ind41_(—)18 cells with the pcg12 chloroplast integrationvector (FIG. 21). Selection of the transformants was on copper-depletedTAP medium containing 100 μg/ml spectinomycin. Colonies resulting fromthe transformation were picked and re-plated three times on TAP-Cu⁺²medium supplemented with 100 μg/ml spectinomycin to ensure completesegregation of the 5′psbD-aadA cassette.

A schematic diagram of the pcg12 vector used in the experiment is shownin FIG. 21. The aadA cassette in the vector is expressed using the psbD5′ UTR. Growth of wild type, Ind41_(—)18, and Ind_aadA_X transgenicstrains is also shown. The strains were serially diluted, then spottedon solid TAP, copper-depleted TAP media (TAP-Cu⁺²), TAP supplementedwith 100-1000 μg/ml spectinomycin (TAP-Cu⁺²+Spc), and TAP-Cu⁺²supplemented with 100-1000 μg/ml spectinomycin (TAP-Cu⁺²+Spc) andcultured for 7-10 days at a light intensity of 100 μE m⁻²s⁻¹.

Screening of transformants was accomplished by replica plating theputative inducible aadA transgenic lines on TAP+Spc100 andTAP-Cu⁺²+Spc100 solid agar medium. All of the colonies tested grewequally well on both culture media, indicating a loss of promotercontrol of the Cyc6Nac2 transgene in these strains (FIG. 21A). However,when higher concentrations of spectinomycin were tested, 85% of thestrains tested were sensitive to spectinomycin when copper wassupplemented in the growth medium, but not when copper was omitted fromthe medium (FIG. 21B). Several of these strains, named Ind_aadA, werechosen for further characterization. The genotype of these strains isnac2::cy6_(Pro)Nac2::5′petA-psbD::5′psbD-aadA.

Growth Analysis of Ind_aadA Transgenic Strains

Growth analysis of several inducible strains retained from the initialscreening process was accomplished by serial diluting, then spottingwild-type, Ind41_(—)18 and Ind aadA cells on either TAP, TAP-Cu⁺², HSM,HSM-Cu⁺² and solid agar medium supplemented with a range ofspectinomycin concentrations (0, 100, 250, 500, 750, 1000, 2000 μg/ml)(FIG. 21B). Of the 11 strains tested in this fashion one, Ind_aadA_(—)36was capable of growing on TAP medium supplemented with >500 μg/mlspectinomycin. On the other hand, 6 of 11 strains tested were able togrow on copper-depleted TAP medium at low spectinomycin concentrationsbut could not grow with spectinomycin concentrations above 250 μg/ml(FIG. 21B). One strain named Ind_aadA_(—)117 was sensitive tospectinomycin when cultured on TAP +250 μg/ml spectinomycin, but wascapable of growing on copper-depleted TAP medium at all concentrationsof spectinomycin tested.

Northern Analysis of Total RNA Extracted from Ind_aadA_(—)117

To gain insight into the induction of aadA expression inInd_aadA_(—)117, total RNA was isolated from Ind_aadA_(—)117 cellscultured in either non-inducing (TAP) or inducing conditions (TAP-Cu⁺²,TAP-Cu⁺² +Spc, TAP-O₂, HSM-Cu⁺²). Northern analysis of these samplesrevealed that psbD transcripts accumulated to the same levels as wasdescribed for the parental strain, Ind41_(—)18 or approx. 25% of thewild-type psbD RNA. As expected, the psbD RNA of Ind_aadA_(—)117 waslarger than wild-type psbD transcripts, indicating that the authenticpsbD gene is no longer present in this strain, a characteristicinherited from the parental strain, Ind41_(—)18 (FIG. 22). Importantly,accumulation of aadA transcripts was observed in all cultures in whichCyc6 transcription was induced (FIG. 22). The “leaky” phenotype of theInd_aadA strains was confirmed by the presence of a small amount of aadARNA in TAP grown Ind_aadA_(—)117 cultures (FIG. 22). Surprisingly, aadAtranscripts were more abundant in anaerobically grown cultures thancopper-starved cultures of Ind_aadA_(—)117, a characteristic not sharedby the “grand-parental” strain cy6Nac2.49 with respect to psbD/D2expression (FIG. 22). In the assay shown in FIG. 22, total RNA wasextracted from wild-type, and Ind_aadA_(—)117 cells cultured in TAP,TAP-Cu⁺², TAP-Cu+2+Spc TAP-O₂ ₊Spc, HSM-Cu⁺² and HSM-Cu⁺²+Spc liquidmedia. Probes are indicated on the left in FIG. 22.

Analysis of Ind_aadA_(—)117 Protein Extracts

Total proteins extracted from Ind_aadA_(—)117 cells were analyzed byimmunoblots using antisera specific for several importantchloroplast-encoded proteins. D2 protein levels were found atapproximately 25% of wild-type levels in all cultures of Ind_aadA_(—)117examined, less than in the parental strain Ind41_(—)18 which accumulated50% of D2 protein (FIG. 23). On the other hand, full restoration of D1and CP47 protein accumulation was observed in most of theInd_aadA_(—)117 protein extracts tested and, in this case, D2 proteinaccumulation was estimated to be reduced by 75%. Therefore,surprisingly, D1 and CP47 accumulation was not adjusted to D2 proteinlevels. Nac2 protein accumulation in Ind_aadA_(—)117 was determinedusing soluble extracts prepared from Ind_aadA_(—)117 cultured under avariety of conditions. Induction of Cyc6Nac2 was observed in solubleextracts from anaerobic and copper-starved Ind_aadA_(—)117, although, asmall amount of Nac2 was detected in TAP grown Ind_aadA_(—)117 cultures(FIG. 23). The presence of trace amounts of Nac2 in TAP cultures, acondition where the transcription of Cyc6 is repressed, demonstratedthat the system was slightly “leaky” in the Ind aadA strains (FIG. 23).Therefore, the initial observation that Ind_aadA transgenic strainscultured on TAP medium were able to grow in the presence of lowconcentrations of spectinomycin is due to some leakiness of Cyc6Nac2. InFIG. 23, total proteins were extracted from wild-type, andInd_aadA_(—)117 cells cultured in TAP, TAP-Cu⁺², TAP-Cu+2+SpcTAP-O₂₊Spc, HSM-Cu⁺² and HSM-Cu⁺²+Spc liquid media and were sizefractionated and immobilized on PVDF membranes. Probes are indicated onthe left of FIG. 23.

aadA Assay of Ind_aadA_(—)17

The amount of aadA was estimated indirectly by measuring its activity(Table 1). The assay is based on the ability of the aadA enzyme totransfer the adenyl moiety of an ATP molecule to spectinomycin, therebyadding a positive charge to the spectinomycin molecule. Positivelycharged spectinomycin molecules can bind a phospho-cellulose membranethat carries a negative charge. Thus, if crude extracts of Chlamydomonasexpressing aadA are incubated in the presence of spectinomycin andα³²P-labeled dATP, the amount of radioactivity present on thephospho-cellulose membranes after spotting the reactions and washing offthe non-specific products provides a relative measure of the activity ofthe aadA enzyme. Crude extracts of Ind_aadA_(—)117 cells cultured ineither TAP, TAP-Cu⁺², TAP-Cu⁺² +Spc liquid media were used to measurethe aadA activity in this transgenic strain compared to the parentalstrain and another strain expressing the traditional aadA cassette inthe wild-type background. The combined results of several independentassays are presented in Table 1. No aadA activity was detected inInd41_(—)18 thus demonstrating that the removal of the cassette in thisstrain is complete. On the other hand, aadA activity in both thewild-type strain expressing the traditional aadA cassette, and inInd_aadA_(—)117 grown in TAP-Cu⁺² and TAP-O₂ was similar to thatpreviously reported for aadA-expressing transgenic strains (Table 1). Asmall but significant aadA activity was also present in crude extractsof Ind_aadA_(—)117 cultured in TAP medium. This result confirmed, that asmall amount of aadA activity was present in uninduced Ind_aadA_(—)117,although the activity was only a fraction of the activity of inducedcultures of Ind_aadA_(—)117.

Screening for strains capable of inducing the expression of the aadAgene using the cy6Nac2 chloroplast inducible gene expression systemconsistently resulted in the recovery of strains that had a “leaky”phenotype. Because the Cyc6Nac2 transgene was demonstrated to be tightlyregulated in the parental strain, de-repression of Cyc6Nac2 transgene inInd_aadA was, by inference, considered a prerequisite for surviving thescreening process. One possible explanation for this observation is thatthere was initially a very small amount of copper contamination in thecopper-depleted medium used at each step in the screening process,including in the media used for the biolistic transformation ofInd41_(—)18 with pcg12. If this was indeed the case, a transientrepression of Cyc6 transcription would be predicted to occur untilcopper contamination dropped below 2×10⁶ ions/cell, and as a result,only those transformants that de-repressed Cyc6Nac2 would survive theoriginal transformation with the pcg12 plasmid. In other words, giventhat repression of Cyc6Nac2 transcription was long enough to negativelyeffect cell survival in spectinomycin-supplemented media; all coloniesthat survived the original transformation were generated from a singlecell that would not have divided unless Cyc6Nac2 had been de-repressed.Contamination of the culture medium was considered to be unavoidable asit has been well documented that even minute concentrations of copperrepress the transcription of Cyc6. Indeed experiments designed to studythe kinetics of copper-mediated repression in cy6Nac2.49 revealed thatre-suspension of copper-starved cy6Nac2.49 cells in copper-depletedmedia, transiently repressed Cyc6Nac2 transcription, as well astranscription of the authentic Cyc6 locus for 1-2 cycles of division.

Nevertheless, the Ind_aad_(—)117 transgenic strain shows that the designfor an inducible chloroplast gene expression system based on thenucleus-encoded Nac2 protein is possible for Chlamydomonas. Thetransgenic Ind41_(—)18 strain can be used to induce the expression ofany chimeric gene driven by the psbD 5′UTR integrated in the chloroplastgenome, provided that the psbD 5402 UTR is capable of driving theexpression of the gene of interest.

For the assays in Table 1, aminoglycoside adenyl transferase activity inInd41_aadA-117 was determined under inducing and repressing conditions.Extracts from WT-aadA, Ind41_(—)18 and Ind41_aadA-117strains wereassayed for aadA activity and for total protein content. The activity isindicated as cpm incorporated per μg of protein. Numbers of independentmeasurements are indicated in parenthesis.

TABLE 1 Strain +Cu −Cu WT  1.4 +/− 2.0 nd WT-aadA 207.0 +/− 49.5 (3)192.6 +/− 51.4 (4) Ind41_18  9.2 +/− 4.1 (4)  12.2 +/− 7.9 (4) Ind41_117 24.2 +/− 12.5 (4) 274.3 +/− 90.6 (7)

Inducible Expression of the VP28_FLAG, IBVD_FLAG, and DILP_FLAG

To test if the inducible chloroplast gene expression system describedhere could be applied to the production of foreign proteins, threedifferent foreign proteins were selected for heterologous expressionusing the 5′ psbD driven transgenes, VP28, DILP, and IBVD. IBVD (or VP2)is used to generate a vaccine for the control of Infectious BursalDisease Virus (IBDV) in poultry (Mundt 1995). VP28, the 23 kD fragmentof a major structural envelope proteins of White spot syndrome virus ofPenaeus monodon, was demonstrated to protect shrimp from infection whenfed as a subunit vaccine (Witteveldt 2004).

Three FLAG-tagged foreign genes VP28, DILP, and IBVD with a codon biasthat was optimized for the C. reinhardtii chloroplast genetic machinerywere provided as a gift from Dr. Stefan Surzycki (Indiana University,Bloomington) and were individually subcloned in the chloroplasttransformation and expression vector pcg12 so that the 5′UTR of psbD wasdriving the expression of the foreign protein with the rbcL 3′UTR as aterminator (FIG. 24A). Because these new constructs lacked a selectablemarker, the generation of transformants required co-transformation withanother chloroplast integration vector carrying a selectable marker(FIG. 24A).

A schematic diagram of the pcg12 _DILP vector used in experiments toinduce the expression of Drosophila insulin-like peptide is shown inFIG. 24A. The black box represents DILP coding sequence. The arrowrepresents the 5′ leader of the psbD gene. The asterisks indicateinsertion of the 3HA-11 epitope. In FIG. 24B, immunoblots using totalproteins extracted from Ind_VP28 (upper left), Ind_IBVD (upper right) orInd_DILP (lower panel) are shown, probed with antibody that recognizedthe FLAG epitope. The predicted molecular weight of the proteins areVP28-23 kD, IBVD-49 kD, and DILP-12 kD and are indicated with anasterisk.

These vectors were co-transformed with the pY1_INT vector, which carriesthe ycf1 gene and flanking chloroplast sequence and the aadA cassettewhich confers resistance to spectinomycin into the Ind41_(—)18 strain.Following selection on TAP plates amended with spectinomycin, putativetransformants were tested for the presence of the gene using PCR witholigonucleotides that amplified the foreign gene. Of the 10 coloniestested by PCR for co-insertion of the transgene, seven were positive forVP28 and DILP and five were positive for the presence of the IBVD gene.These lines were named IndVP28_x, IndDILP_x and IndIBV_x and had thegenotype of nac2.Cyc6_(pro)Nac2::5′petA-psbD::5′psbD-VP28/DILP/IBVD.

Colonies that tested positive for the insertion of the foreign gene inthe chloroplast genome were tested for protein production usingimmunoblot analysis with the Flag® antibody following induction of thegene by copper starvation. Of the 22 transgenic lines tested in thisway, 8 of 8 appeared to accumulate the VP28 protein, as a 23 kD proteinwas induced in extracts from IndVP28 that was not present in either thewild-type or the non-induced controls (FIG. 24B—Upper left). Totalprotein extracted from 4 of 6 IndDILP strains analyzed also accumulateda >25 kD protein when these cells were induced (FIG. 24B—Lower panel). A50 kD protein accumulated in 3 of 7 IndIBVD strains assayed in this way(FIG. 24B—Upper right).

FIG. 25 shows based on immunoblots with total proteins extracted fromIndDILP strains that the expression of DILP_FLAG was induced in initialscreening experiments. IndDILP strains were cultured in either TAP (ui)or TAP-Cu⁺² (i) liquid media supplemented with 50 μg/ml spectinomycinand size fractionated on 15% SDS-PAGE gels. The resulting immunoblotswere then incubated with antibodies that recognized the FLAG epitope.Total proteins extracted from a transgenic strain that expressed aFLAG-tagged Alb3.1 protein were used as a positive control for thedetection of the FLAG epitope in the experiment. The asterisk indicatespredicted size of the DILP_FLAG peptide inserted in the pcg12_DILPvector.

Proteins extracted from three IndDILP lines shown to express the DILPprotein were characterized further by comparing the proteins extractedfrom these strains when Cyc6 transcription was repressed versus induced.Of the four IndDILP strains tested, two seemed to correctly induce theproduction of DILP_FLAG, as a 12 kD protein. Therefore, the chloroplastinducible expression system developed here induced the expression ofDILP. This finding was particularly interesting as previous attempts toexpression the DILP protein in a constitutive fashion in thechloroplasts of Chlamydomonas reinhardtii never resulted in a high levelof expression (Stefan Surzycki, personal communication). Thus, theinducible chloroplast gene expression system may provide a commerciallyrelevant tool for the inducible expression of foreign proteins,especially those proteins resistant to constitutive expression.

EXAMPLE 6 Expression of Genes that Affect Hydrogen Production

Strains and Media

The nac2-26 mutant strain was previously described (Kuchka, et al. EMBOJ. 7, 319-324; Nickelsen, et al. EMBO J. 13, 3182-3191). The cyc6Nac2.49strain contains a trans-gene consisting of the Cyc6 promoter fused tothe Nac2 midi-gene inserted into the nuclear genome of the nac2-26mutant (Δnac2::cy6proNac2). Ind41 was derived from cy6Nac2.49 byreplacing the psbD promoter and 5′UTR with a 675 fragment containing thepetA promoter and 5′UTR (Δnac2::cy6pro Nac2::5′petA-psbD). Ind41-18 isrelated to the Ind41 strain, except that the aadA cassette in theInd41-18 strain has been completely excised from the chloroplast DNA andthe strain is therefore sensitive to spectinomycin(Δnac2::cy6proNac2::5′petA-psbD[Spc^(S)]). Ind_aadA_(—)117 was derivedfrom Ind41-18 and contains the aadA cassette driven by the psbD promoterand 5′UTR inserted downstream of the atpB gene(Δnac2::cy6proNac2::5′petA-psbD::5′psbD-aadA). All strains weremaintained on TAP (Tris-acetate-phosphate) medium supplemented with 1.5%Bacto-agar at 25° C. under dim light. In experiments wherecopper-supplemented or copper-deficient (—Cu⁺²) solid agar and liquidTAP and HSM medium was employed, medium was prepared according to Quinnand Merchant (Methods in Enzymol. 297, 263-279). TAP and TAP-Cu⁺² mediawas supplemented with 100 μg/ml spectinomycin (Sigma-Aldrich) or 20μg/ml paromomycin (Sigma-Aldrich) where necessary. In experiments wherecells were deprived of oxygen, liquid cultures where bubbled with N₂ gaswith 150 rpm/min agitation and constant light illumination (20μE/m⁻¹s⁻²). Cell density was determined using a hemacytometer.

Plasmid Construction

Standard techniques were used to manipulate and analyze all plasmidconstructs. Sequencing of constructs was carried out using BigDyeterminator sequencing kit (Applied Biosystems, La Jolla, Calif.) and anABI Prism 377 automated sequencing machine (ABI). The bacterial hostused for cloning in E. coli was DH10B (Amersham Biosciences). Alloligonucleotides were ordered from Microsynth GmbH (Balgach, CH).

Transformation of Chlamydomonas Cells

Nuclear transformation of Chlamydomonas reinhardtii strains nac2-26 wasperformed by electroporation essentially as described in Shimogawara, etal. Genetics 148, 1821-8.

Chlorophyll and Oxygen Evolution Rate Measurements

Oxygen evolution and respiration rates were determined using a Clarktype oxygen electrode attached to a X type light source at 25° C.(Hansatech Instruments Ltd., Norfolk, UK).

Hydrogen Measurements and Calculations

All liquid phase and gas phase measurements of N₂, O₂, H₂ and CO₂ wereperformed as follows. Continuous monitoring of dissolved gases were madeusing a sealable, thermo-stated Clarks type vessel where gases were fedinto the ion source of a mass spectrophotometer (model MM 880; VGInstruments, Cheshire, United Kingdom) through a polypropylene membraneunder continuous agitation and constant illumination using a fiber-opticilluminator (model KL 1500, Schott, Mainz, Germany). In experimentswhere transcription of the Cy6Nac2 transgene was repressed, 12 μM copperwas added to the growth medium within the vessel (TAP-Cu⁺² to TAP).Calibration of the mass spectrometer before all gas phase time-pointswas achieved through injection of air and pure hydrogen gas samplesdirectly into the ion source.

Assay for aadA Activity

Assays for aadA activity were carried out on wt, Ind41-18, andInd_aadA_(—)117 strains essentially as described inGoldschmidt-Clermont, Nucleic Acids Res 19, 4083-9. except that³²P-labeled dATP was used in place of the radiolabeled rATP used in theoriginal experiments.

Plasmid Constructions—pRS1_rcy_aadA Construction

The plasmid pKS-108#14 was used for the construction of plasmidpRS1_rcy_aadA. The pKS-108#14 plasmid contains the chloroplast DNA EcoRIR3 fragment of C. reinhardtii, with the aadA cassette inserted atposition −263 bps relative to the psbD ATG initiation codon. In order toreplace the psbD 5′UTR with the petA 5′UTR, a 943 by chimeric DNAfragment comprised of the petA 5′UTR fused to the coding sequence ofpsbD was generated using overlap-extension PCR with oligonucleotidesRS1, RS2, RS3 and RS4 (Table2). The resulting PCR product was digestedwith PvuII/ClaI restriction endonucleases and ligated into plasmidpKS-108#14 digested with the same enzymes to generate the pRS1 plasmid.The design of the chloroplast inducible expression system involves twosuccessive chloroplast transformations which would require two differentselectable markers. Alternatively, recycling of aadA is possible using amodified aad4 cassette that is flanked by 483 by direct repeats,allowing for the efficient removal of the cassette by homologousrecombination after the selective pressure has been removed. Cloning ofthe recyclable aadA cassette into pRS1 was achieved by first cutting pRS1 with ClaI and SphI, and then filling the 5′ and 3′ ends of theresulting 6.3 kb plasmid with T4 DNA polymerase. This resulted in theexcision of the atpA promoter and 5′UTR fused to the aadA codingsequence from the pRS1 plasmid, but did not remove the 3′ sequence ofrbcL. Insertion of the recyclable cassette into pRS1ΔaadA was achievedby first excising the recyclable aadA cassette from pKS-483-aadA-483plasmid using SacI and KpnI restriction endonucleases and blunting bothends with T4 DNA polymerase and PNK kinase. Blunt end ligation of the2.8 kb recyclable aadA cassette into pRS1ΔaadA was accomplished togenerate pRS1_rcy_aadA (FIG. 27).

Construction of pcy6Nac2(paroR)

To construct a plasmid with the 428 by Cyc6 promoter sequence fused inframe with the Nac2 coding sequence, a 5.1 kb chimeric midi-gene of Nac2was employed. In brief, the plasmid pKS(−)nac2(midi) contains 3.0 kb of5′ Nac2 genomic sequence ending at the SfrI restriction site within theNac2 coding sequence fused to a 1.96 kb Sfr1/XhoI fragment containingthe 3′ cDNA sequence tagged with 3 HA, 6 His (SEQ ID NO: 1) and 9 Mycepitopes, introduced in frame with the Nac2 coding sequence justupstream of the stop codon. In order to place the Nac2 gene under thecontrol of the Cyc6 promoter, a chimeric DNA fragment comprising theCyc6 promoter fused to the coding sequence of Nac2 was generated byoverlap-extension PCR using 4 oligonucleotides specific for the Cyc6promoter element and Nac2 genomic DNA. The resulting PCR fragmentconsisted of the 428 by Cyc6 promoter fragment fused in frame with an833 by genomic Nac2 fragment. The PCR fragment was then cloned into thepNac2(midi) plasmid using the unique restriction sites XbaI and AatII ofpKS(−)Nac2(midi). Finally, the 5.8 kB Cyc6Nac2 trans-gene was clonedinto the pSL17 plasmid using the unique sites EcoRI and XbaI of pSL17.This plasmid contains the aphVII cassette conferring resistance toparomomycin. The resulting 10.8 kb plasmid, pcy6Nac2(paroR), was used totransform nac2-26 mutant cells.

Transformation of Chlamydomonas Cells

Cells of nac2-26 cells were grown in TAP medium, harvested in mid-logphase (2-4×10⁶ cells/ml), and treated with gamete autolysin, thenre-suspended in TAP+40 mM sucrose medium. For each electroporation, 10⁸treated cells were incubated with 2.5 linearized pcyc6Nac2(paroR) orpSL17 plasmid DNA (to determine electroporation efficiency), plus 50 μgsalmon sperm DNA, then transformed by electroporation in a 0.2 mlelectroporation cuvette (Biorad, USA) using the Biorad (SIC) set to 0.75kV, 25 μF and no resistance (Biorad, USA). The treated cells wererecovered in 1 ml fresh TAP, 40 mM sucrose, 0.4% PEG-8000, 20% starchmedium for 10 minutes, and plated on TAP medium supplemented with theantibiotic paromomycin (20 μg/ml). Paromomycin resistant colonies werescreened for the ability to grow photo-autotrophically on minimal mediumlacking copper (HSM-Cu⁺²) at 25° C. in high light (45 μEm⁻²s⁻¹).Photo-autotrophic strains were then tested for the ability/inability togrow on minimal medium (HSM).

Chloroplast biolistic transformation of Chlamydomonas was performed witha helium-driven particle gun. 10⁸ cells of TAP-grown cy6Nac2.49 wereplated on solid agar TAP supplemented with 100 μg/ml spectinomycin(TAP+Spc100) and bombarded with tungsten particles coated with 1 μgpRS1_rcy_aadA plasmid DNA. After 2 weeks in dim light (5 μEm⁻²s⁻¹),single colonies were picked and re-cloned four times on TAP+Spec 100medium, then cultured at 25° C. in dim light (5 μEm⁻²s⁻¹) to ensure thatthe strains were homoplasmic for the selectable marker. To test forphoto-autotrophic growth, cells were plated on solid HSM medium andgrown at 25° C. under medium light (45 μEm⁻²s⁻¹). In the case oftransformation of Ind41_(—)18, 10⁸ TAP-Cu⁺² cells were plated on solidTAP-Cu⁺² medium supplemented with 100 μg/ml spectinomycin (TAP-Cu⁺²+Spc100) and bombarded with tungsten particles coated with 1 μg pcg12plasmid DNA. After 2 weeks in dim light (5 μEm⁻²s⁻¹), single colonieswere picked and re-plated three times on TAP-Cu⁺²+Spc 100 medium andcultured at 25° C. under dim light (5 μEm⁻²s⁻¹).

Growth Analysis

For growth analysis of wt, nac2-26, cy6Nac2.49 strains, cells were grownin TAP-Cu⁺² medium to a density of 2-4×10⁶ cells/ml, then diluted to adensity of 1×10⁶ cells/ml, followed by 10× serial dilution so that thefinal dilution was estimated to contain 100 cells when plated. Ten μlaliquots of each dilution were then spotted onto the appropriate solidagar plates, and grown under high light at 25° C. for 10 days. In thecase of the Ind41 and Ind41-18 strains, 10³ cells were plated on theappropriate medium and cultured at 25° C. under continuous illumination(100 μEm⁻²s⁻¹) for 10 days. For growth analysis of the inducible aadAtransgenic lines, experiments were performed. In brief, wt, Ind41-18 andInd_aadA transgenic lines were grown in either TAP-Cu⁺² or TAP liquidmedium then transferred 3 times to either fresh TAP-Cu⁺² or TAP liquidmedia. Serial dilutions of TAP and TAP-Cu⁺² grown cultures were platedon TAP medium or TAP-Cu⁺² solid agar plates supplemented with increasingconcentrations of spectinomycin (0-1000 μg/ml) and cultured at 25° C. inunder continuous illumination (100 μEm⁻¹s⁻²) for 10 days.

Fluorescence Transients

Fluorescence transients were performed. Cells grown on TAP agar in darkwere analyzed with a Plant Efficiency Analyzer (PEA, HansatechInstruments, UK) after dark adaptation for 5 minutes.

RNA Analysis

Isolation of total RNA from wt, nac2-26, cy6Nac2.49, Ind41_(—)18 andInd_aadA_(—)117 strains was achieved using the RNA Plant Mini RNAextraction kit according to manufacturer's instructions (Qiagen Ghmb,Germany). In the case of RNA samples taken during time courseexperiments, 10⁸ cells were centrifuged at 3000 g and processed usingRNAeasy RNA protection solution according to manufacturer's instructions(Ambion, USA).

RNA blot analysis was performed. RNA (2 μg) was electrophoresed in a1.2% agarose-4% formaldehyde gel in 1× MOPS buffer, then transferred toa Hybond N+ nylon membrane (Amersham, USA) in 20×SSC buffer andUV-cross-linked to the membrane using a Stratalinker cross-linking oven.Pre-hybridization and hybridization of the membrane was carried out at65° C. in modified Church's hybridization solution (0.5 M phosphatebuffer (pH 7.2), 7% SDS (w/v), 10 mM EDTA). A 380 by DNA fragment ofpsbD was isolated by digesting plasmid pks-108#14 with AccI and StyI foruse as a probe and labeled with [α³²P]dATP using the random primingtechnique. The 685 bps DNA fragment of Cyc6 cDNA was labeled with[α³²P]dCTP using the random priming technique. A 804 NcoI/SphI fragmentof aadA coding sequence was isolated by digestion of the pcg12 plasmidfor use as a probe and labeled with [α³²P]dATP using the random primingtechnique. A 693 bps fragment of atpB was isolated by digesting pcg12with EcoRV and HpaII for use as a probe and labeled with [α³²P]dATP byrandom priming. After hybridization, membranes were washed at 65° C. for10 min with high stringency washing buffer [0.1% SDS, 0.1% SSC].

Protein Analysis

Total protein extracts of Chlamydomonas strains wt, nac2-26, cy6Nac2.49,Ind41_(—)18, and Ind_aadA_(—)117 were prepared by collecting 3×10⁶ cellsin a 1.5 ml Eppendorf tube and resuspending the pellet in a 2× solutionof Sigma protease inhibitor cocktail (Sigma-aldrech, USA) followed bylysis in an equal volume of cell lysis buffer (100 mM Tris-HCl pH 6.8,4% SDS) at 37° C. for 30 minutes. To pellet cell debris, the sampleswere centrifuged at 10,0000 g for 5 min and the supernatant was used astotal protein extract. To determine protein concentration 5 μl ofsupernatant was assayed using Bradford method (Bio-Rad Protein Assay,BioRad, USA).

For immunoblot analysis, 20 μg total protein was separated on a 12% SDSpoly-acrylamide gel and transferred to Protran 0.45 μm nitrocellulosemembrane (Schleicher and Schuell). When Nac2 antibody was employed, 80μg protein was loaded on 8% poly-acrylamide gels. Membranes were blockedin Tris-buffered saline solution (containing 5% of non-fat dry milk and0.1% Tween-20 (TBS-T). For the primary antibody reaction, dilution inTBS-T was as follows: D2 antibody, 1:10,000 dilution; D1, antibody1:10,000; Nac2 antibody, 1:10,000; PsaA antibody, 1:10,000; AtpBantibody, 1:10,000; RUBISCO-Holo antibody, 1:50,000. Incubation wasperformed for 1 hr at room temperature. Subsequently, the membrane waswashed five times for 5 minutes in TBS-T containing 1% non-fat dry milk.For the secondary antibody reaction, the membrane was incubated for 1 hrat room temperature with peroxidase-linked anti-rabbit IgG (in TBScontaining 1% non-fat milk) at a final antibody dilution of 1:10,000.The membrane was washed 5 times for 5 minutes in TBS and the signal wasvisualized by enhanced chemiluminescence.

Copper-mediated Repression and Time-course Experiments

To follow the copper-mediated repression over time of Cy6Nac2 in thecy6Nac2.49 transgenic strain cy6Nac2.49 cells were grown in TAP-Cu+2medium to a density of 4×10⁶ cells/ml, diluted in fresh TAP-Cu+2 mediato a density of 5×10⁵ cells/ml, then split into two independentcultures, one of which was left untreated while the other had copperadded to the growth medium to a final concentration of 6 μM. Time pointswere then taken for each culture every 8 hours for 40 hours. Twoindependent samples were used for F_(V)/F_(M) measurements and theaverage for each culture was determined at the indicated time points.

Experiments to test the copper-mediated induction of cy6Nac2.49 werecarried as described for the copper-mediated repression experimentsexcept that pre-cultures of cy6Nac2.49 were grown in TAP medium and thecells were washed two times in copper-depleted medium before dilution inTAP-Cu⁺² medium at a concentration of 5×10⁵ cells/ml. To initiate thetime course experiment, cells were split into two separate cultures andcopper was added to a final concentration of 6 μM in one of them.

Hydrogen Measurements

The hydrogen production in the cy6Nac2.49 strain was compared with thatof the wild type under sulfur deprivation. In the cy6Nac2.49 cultureused in FIG. 32, 20 μmol H₂/L was produced during one cyclecorresponding to a maximal rate of 1 mmol H₂ mol⁻¹ Ch1 s⁻¹. These ratesvaried from one experiment to another and reached in some cases 3.1 mmolH₂ mol⁻¹ Ch1 s⁻¹. Under conditions permissive for photosynthesis(Cu-deprived medium) the net rate of oxygen evolution was 23 mmol O₂mol⁻¹ Ch1 s⁻¹ in Cy6Nac2.49 cells. This rate was 1.5-2 fold higher inwild-type cells. Thus, the maximal rate of hydrogen production rangedbetween 4 and 13% of the rate of net oxygen production. In the case of aculture subjected to sulfur starvation for 100 hrs, the average valuecan be estimated at 4 mmol H₂ mol⁻¹ Ch1 s⁻¹. If one compares the 20 μmolH₂/L produced by cy6Nac2.49 cells during one cycle with the 4 mmol H₂/Lproduced during 100 hrs in a sulfur-starved wild-type culture, it isapparent that in order to achieve a similar hydrogen production, thecy6Nac2.49 system still needs further improvement, either a higherefficiency per cycle or a close enchainment of cycles. It is inprinciple possible to modify genetically Chlamydomonas so as to improvehydrogen production e.g. by using state transition mutants blocked instate 1 which are unable to perform cyclic electron flow or by drivingone of the Calvin-Benson enzymes with the Cyc6 promoter. In this waycarbon assimilation would be diminished at the same time as PSIIactivity and competition for electrons during the hydrogen productionphase would be decreased.

TABLE 2 List of oligonucleotides. Sequence 5′−>3′ (SEQ ID NOS: 2-8, respectively, in order Restriction Name of appearance) Site RS1 5′GG

GCAGGCAGTGGCGGTAC EcoRI C3′ RS2 5′GATATGTACCGATCGCAATTGTCAT N/AAATTTTATTAATCTTAAAAC3′ RS3 5′GTTTTAAGATTAATAAAATTATGAC N/AAATTGCGATCGTACATATC3′ RS4 5′GG

TTAAGAAGTTACAACCT PvuII TC3′ Cy6Pro-1 XbaI Nac2- 5′CGGTAGAGCCCC

GATGGAG NdeI Cyc6-1 TAGGT3′ Nac2- 5′ACCTACTCCATC

GGGGCTC NdeI Cyc6-2 TA3′ Nac2(+1260) 5′ACCACAGAGCCCTGCCAG 3′ N/A

No natural inducible chloroplast gene expression system is available forChlamydomonas. Such a system was developed by taking advantage of theproperties of the nucleus-encoded chloroplast Nac2 protein. This proteinis required for processing and stable accumulation of the psbD mRNAwhich encodes the D2 reaction center polypeptide of PSII. The targetsite of Nac2 is comprised within the 74 nucleotide psbD 5′UTR. Fusion ofthis 5′UTR to another coding sequence renders expression of this genedependent on Nac2. The Nac2 coding sequence has been fused to the Cyc6promoter of the cytochrome C₆ gene whose expression is induced by copperdepletion, anaerobiosis and also by addition of nickel, but which isrepressed under copper replete conditions. Because of the specificity ofNac2 for the psbD 5′UTR, this system can be used in principle for theinducible expression of any chloroplast gene by fusing its codingsequence to the psbD 5′UTR.

As described above, the Cyc6-Nac2 construct was inserted into a plasmidcontaining the aphVIII gene conferring resistance to paromomycin (FIG.28A). This plasmid was used for transformation of the Chlamydomonasnac2-26 mutant using paromomycin resistance for selection. Amongst 55transformants tested, two displayed proper control of Nac2 expression bycopper. The growth properties of one of these transformants, cy6Nac2.49,of WT and of the nac2-26 mutant are discussed above (FIG. 28B). Asexpected, all three strains grow on TAP medium with and without copperand the transformants also grow in the presence of paromomycin becausethey contain the selectable marker aphVIII. Only WT cells grow onminimal medium containing copper. However, growth of the cy6Nac2.49strain is restored on minimal medium lacking copper. Growth can also berestored by adding nickel because the Cyc6 promoter is induced by thismetal. The level of psbD expression was determined by RNA blothybridization under different growth conditions (FIG. 28C). As expectedpsbD RNA is undetectable in the nac2-26 mutant strain. In contrast inthe cy6Nac2.49 strain, expression of psbD follows that of Cyc6 and isinduced in the absence of copper or under anaerobic conditions (FIG.28C). The level of the psbD product D2 was examined by immunoblottingusing D2 antiserum (FIG. 28D). D2 protein is undetectable in nac2-26cells grown on TAP plates under all conditions. However in cy6Nac2.49,it accumulates to 20% of wild-type levels when cells are grown in theabsence of copper or under anaerobic conditions (FIG. 26). On minimalmedium the induction of D2 is slightly lower. As expected other PSIIproteins such as CP47 follow a similar pattern as D2 because it is knownthat these proteins are unstable in the absence of the D2 protein. Incontrast the level of the Rubisco protein (RbcL) is not affected innac2-26 (FIG. 28D).

To assess the time required to deplete cells of PSII upon arrest of Nac2synthesis, cells of cy6Nac2.49 were first grown in copper-depleted TAPmedium. Under these conditions PSII is synthesized and accumulates. Theculture was split in half and one culture was maintained under copperdeprivation whereas copper was added to the other culture. The timecourse of cell density and the F_(V)/F_(M) ratio (variable/maximalfluorescence), which provides an estimate of PSII quantum yield, wasdetermined at various time points (FIG. 29A). In the presence of copperthe F_(V)/F_(M) ratio declined to a minimal value within 32 hours.During this period, cells divided 3-4 fold under both conditions andreached stationary phase. Cell extracts were prepared at various timesfor RNA and protein analysis. The levels of Cyc6 and psbD RNA weresignificantly decreased 8 hrs after copper addition and wereundetectable thereafter (FIG. 29B). Other chloroplast RNAs (atpB, rRNA)were stable under these conditions. Immunoblotting revealed that theamount of D2 diminished after copper addition with a lag compared to thedecrease of its mRNA (FIG. 29C) and the other PSII core protein D1 alsodecreased. As expected a decrease in Nac2 was also observed. In contrastchloroplast proteins from PSI (PsaA) and Rubisco were stable (FIG. 29C).

In a reciprocal experiment, cells grown in the presence of copper weretransferred to TAP medium lacking copper and the time course of celldensity and of F_(V)/F_(M) was determined. F_(V)/F_(M) started toincrease only after a lag of 25 hours which is presumably due to thetime needed to deplete the internal cellular copper reserve (FIG. 30A).RNA and protein from cell extracts at different time points wereexamined by RNA blot analysis and protein immunoblotting (FIG. 30B, C).While the Cyc6 RNA was detectable after 16 hours, there was a delay inpsbD RNA accumulation and PSII activity presumably due to the fact thata threshold level of Nac2 is required for the accumulation of psbD mRNAand D2 synthesis.

Inducible Expression of Chloroplast Genes Unrelated to PSII

While the Nac2 system can be used to deplete PSII in a reversiblemanner, we tested whether it can be extended to any other chloroplastgene. This is in principle possible because the Nac2 protein actsspecifically on the psbD 5′UTR and can drive chimeric psbD 5′UTRreporter genes. Hence it should suffice to fuse the psbD promoter and5′UTR to the gene of interest. However, under those conditions PSII nolonger accumulates because of the nac2-26 mutation which leads to theloss of psbD RNA. To circumvent this situation, the petA promoter and 5′UTR were fused to the psbD coding sequence and this construct wasintroduced into a modified version of the p108-14 chloroplasttransformation vector. In this vector the recyclable aadA cassette isinserted upstream of the psbD gene which is driven by the petA promoterand 5′UTR (FIG. 27A). This DNA was inserted into the chloroplast genomeby biolistic transformation using the aadA cassette as selectablemarker. In this way the endogenous psbD gene was replaced by thepetA-psbD construct and thus accumulation of its transcript was nolonger dependent on Nac2. Transformants were restreaked three times onspectinomycin plates and the homoplasmicity was tested by DNA blot andPCR analysis and one of the transformants, Ind41 was selected. The aadAcassette used was flanked by two repeats. To allow for the excision ofthe cassette, the homoplasmic transformant Ind41 was plated repeatedlyon medium lacking spectinomycin. In this way a strain was obtained,Ind41_(—)18, which is sensitive to spectinomycin because it lacks theaadA cassette. The growth properties of Ind41, Ind41_(—)18 andcy6Nac2.49 were tested on different media (FIG. 27B). As expected Ind41grows in the presence of spectinomycin in contrast to Ind41_(—)18 whichis sensitive to the antibiotic. Moreover both Ind41 and Ind41_(—)18 growon HSM minimal medium with or without copper. RNA blot analysis revealedthat the chimeric petA-psbD RNA in Ind41_(—)18 accumulates under allconditions independent of the Cyc6 RNA level (FIG. 27C). The psbD RNA islarger because the size of the petA 5′UTR exceeds that of the psbD5′UTR. Immunoblot analysis revealed that D2 and D1 proteins accumulateto the same level under all conditions tested, in particular when Nac2is not expressed (FIG. 27D).

Next, the aadA cassette fused to the psbD promoter and 5′UTR wasintroduced into this strain by transformation using the cg12 vector(FIG. 31A). Growth of the transformants Ind_aadA-117 and of Ind41_(—)18was tested on TAP plates containing increasing amounts of spectinomycinwith and without copper (FIG. 31B). All strains grow in the absence(FIG. 31B) or presence of copper. As expected the Ind_aadA-117 grows onspectinomycin plates at concentrations of 250 μg/ml or higher only inthe absence of copper. A faint growth was also observed in the presenceof copper on plates containing 100 μg/ml spectinomycin. RNA blotanalysis revealed that aadA RNA accumulates only under inducingconditions for the Cyc6 promoter (FIG. 31C). Protein levels of D2, D1,CP47, and RbcL were largely unaffected but Nac2 was only detected underinducing conditions (FIG. 31D). Because of a lack of reliable aadAantibody, the amount of this protein was assayed by measurements ofaminoglycoside adenyl transferase activity. The activity wassignificantly elevated under conditions when Nac 2 is expressed (Table3).

TABLE 3 Aminoglycoside adenyl transferase activity in Ind41_aadA-117under inducing and repressing conditions. Strain +Cu −Cu WT-aadA 207.0+/− 49.5 (3) 192.6 +/− 51.4 (4) Ind41_18  9.2 +/− 4.1 (4)  12.2 +/− 7.9(4) Ind41_117  24.2 +/− 12.5 (4) 274.3 +/− 90.6 (7)

Extracts from WT-aadA, Ind41_(—)18 and Ind41_aadA-117strains wereassayed for aadA activity and for total protein content as describedabove. The activity is indicated as cpm incorporated per μg protein.Numbers of independent measurements are indicated in parenthesis.

The Inducible Chloroplast Gene expression System can be Used to TriggerHydrogen Production

Chlamydomonas is able to induce hydrogenase and produce hydrogen underanaerobic conditions in the light. It was therefore tested whether theinducible Nac2 system could be used to turn off PSII activity and O₂evolution, so that respiration would lead to anaerobic conditionssuitable for induction of hydrogen production. Cells of cy6Nac2.49 weregrown in TAP medium lacking copper to a concentration of 2×10⁶ cells/ml.Copper was added and the cells were transferred into a chamber connectedto a mass spectrometer and illuminated with white light (250 μE m⁻²s⁻¹).In this system the bottom of the chamber is sealed with a polypropylenemembrane which allows dissolved gases to diffuse directly into the ionsource of the mass spectrometer. In this way the abundance of O₂ and H₂could be measured at discrete time intervals. Because the chamber wasclosed and because copper repressed the synthesis of PSII, O₂ evolutiondiminished. Within a period of 200 min the O₂ was consumed byrespiration. An anaerobic state was reached which led to the synthesisof active hydrogenase and H₂ production (FIG. 32A). The maximal rate ofhydrogen production ranged between 1 and 3.1 mmol H₂ mol⁻¹ Ch1 sec⁻¹,slightly lower than that obtained with sulfur-starved cells, and of muchshorter duration (around 1.5 h vs 3-4 days).

An interesting feature of the Cyc6 promoter is that it is also inducedunder anaerobic conditions even in the presence of copper. It wouldtherefore be expected that once anaerobic conditions have been reachedand hydrogenase is induced in cy6Nac2.49 cells, Nac2 synthesis resumes,PSII is synthesized and oxygen levels rise thus inactivating hydrogenaseand blocking hydrogen production. This was observed. PSII synthesis wasswitched on during the anaerobic hydrogen production phase withconcomitant O₂ evolution and inactivation of hydrogenase so that thehydrogen levels remained constant (FIG. 32A). As a control, the samecell culture was examined without addition of copper. Under theseconditions no hydrogen was produced (FIG. 32B) with a constantproduction of O₂ and a gradual decrease of CO₂ as observed in thecopper-treated cells. Because the Cyc6 promoter is expected to beswitched off under aerobic conditions in copper-replete medium, a newcycle of hydrogen production would be expected. To test this possibilityfurther cy6Nac2.49 cells were grown in TAP medium lacking copper in asealed vessel for 50 hrs and measurement of hydrogen and oxygen wereperformed by mass spectrometry. The results suggest that two successivephases of hydrogen and oxygen production occurred.

Although the invention has been described in detail with reference tocertain preferred embodiments, variations and modifications exist withinthe scope and spirit of the invention as described and defined in thefollowing claims.

What is claimed is:
 1. A method for expressing a heterologous protein inthe plastid of a cell, the method comprising the steps of providing aChlamydomonas cell that comprises in its plastid a construct comprisinga promoter and a psbD 5′UTR operably linked to a nucleic acid encoding aheterologous protein; introducing into the nucleus of the cell arecombinant nucleic acid comprising an inducible promoter operativelylinked to a nucleic acid encoding Nac2; contacting the cell with aninducer or treating the cell under conditions that result in the removalof a repressor; wherein the inducer or the repressor associates with theinducible promoter in the nucleus; wherein association of Nac2 with themRNA encoding the heterologous protein enhances expression of the mRNA,resulting in the production of the heterologous protein in the plastid.2. The method of claim 1, wherein the cell has an inoperative or missingcopy of the endogenous nucleic acid encoding Nac2.
 3. The method ofclaim 1, wherein the plastid is selected from the group consisting of achloroplast, a leucoplast, an amyloplast, an etioplast, an elaioplast,and a chromoplast.
 4. The method of claim 1, wherein the induciblepromoter has the sequence of SEQ ID NO:11.
 5. The method of claim 1,wherein the inducer is a reduction in the concentration of oxygen to apredetermined level.
 6. The method of claim 1, wherein the inducer isapplied and removed for a plurality of cycles, wherein a cycle comprisesapplying and removing the inducer.
 7. The method of claim 1, wherein theheterologous protein is selected from the group consisting of apharmaceutical agent, an industrial enzyme, an enzyme involved inchloroplast maturation or degradation, a nutraceutical, a defenseproduct for the cell, an enzyme involved in amino acid synthesis, aprotease, an antibody, a vaccine, and an antimicrobial agent.
 8. Asystem for expressing a heterologous protein in the plastid of arecombinant Chlamydomonas cell, the system comprising an exogenouslyadded or removed inducer for an inducible promoter; and a Chlamydomonascell that comprises in its plastid a construct comprising a promoter anda psbD 5′UTR operably linked to a nucleic acid encoding a heterologousprotein and comprises in its nucleus a recombinant nucleic acidcomprising the inducible promoter operatively linked to a nucleic acidencoding Nac2.
 9. The system of claim 8, wherein the cell has aninoperative or missing copy of the endogenous nucleic acid encodingNac2.
 10. The system of claim 8, wherein the plastid is selected fromthe group consisting of a chloroplast, a leucoplast, an amyloplast, anetioplast, an elaioplast, and a chromoplast.
 11. The system of claim 8,wherein the inducible promoter has the sequence of SEQ ID NO:11.
 12. Thesystem of claim 8, wherein the inducer is a reduction in theconcentration of oxygen to a predetermined level.
 13. The system ofclaim 8, wherein the heterologous protein is a protein involved in theproduction of hydrogen gas.
 14. The system of claim 8, wherein theheterologous protein is selected from the group consisting of apharmaceutical agent, an industrial enzyme, an enzyme involved inchloroplast maturation or degradation, a nutraceutical, a defenseproduct for the cell, an enzyme involved in amino acid synthesis, aprotease, an antibody, a vaccine, and an antimicrobial agent.